Appendix C. Use of MAExplorer with user's microarray data
This section discusses the use of MAExplorer to convert microarray
data from a variety of sources including various types of labeling
33P-labeled, biotin-labeled, or Cy3/Cy5 ratio-labeled
spotted membranes or glass slides or oligo-chips of different
geometries and numbers of duplicate spots/gene.
Note: This appendix contains a "computerese" description on how
to use MAExplorer with your array data. The user-friendly "wizard"
tool  Cvt2Mae makes it much easier for most molecular
biologists to use. Cvt2Mae is available for download on the
MAExplorer home page. This appendix gives some examples below of some of the required
file data for those of you who want to understand the data file
formats or want to manually convert your data or use your own
conversion program on your data. Note that you do not need to read
this chapter to use MAExplorer if you use the Cvt2Mae converter, use
some other conversion software (eg. the NCI/CIT mAdb array database
server), etc.
|
MAExplorer requires a specification of array geometry and
quantification information. These are defined in a
configuration startup file. The startup file contains the
initial list of hybridized samples to be loaded, and other
parameters such as the name of the configuration file (if it is
different from the default name). A stand-alone application causes the
.mae startup file (or the PARAM list in the case of an applet) to
be read when it is started. The configuration file contains various
defaults. If any of these are specified in the configuration file, the
override the built in default values. Values from the .mae startup or
applet PARAMs will override the configuration file values. These
configuration parameters may be overwritten by arguments in the
stand-alone .mae startup files or PARAMs in the Applet startup
specifications.
A few additional files are required and are defined in the
configuration file. These include: a Gene-In-Plate-Order or
GIPO file; a samples database file listing names of the
samples available for loading; and a gene class names
file. An optional (but deprecated) extra array information file
may be specified to access additional data about samples. Quantified
hybridized sample array spot data (Quant files) from each array
is put into a separate data file. Note that all data files are
tab-delimited files such as may be generated with Excel, relational
databases or directly from array spot quantification software.
Hybridized sample arrays must be scanned and then spots quantified
using other software. MAExplorer does not do spot quantification from
scanned image files. However, MAExplorer can use spot data from a
variety of array image quantification programs that generate
tab-delimited data files. The data needs to be converted to the
MAExplorer schema described in this Appendix.
The derivation of quantified spot data
files from hybridized sample arrays is discussed later in this
section as are in the quant file data
format.
The configuration file is created once for each new array GIPO
geometry and database of hybridized samples. It is independent
of the number of samples. Configuration parameters include array
geometry (# of grids, # of duplicate spots/gene, etc), whether the
data is intensity or ratio data (e.g. Cy3/Cy5), etc. The configuration
file may also include labeling, quantification dynamic range, default
analysis thresholds, mapping of used data file table-field names to
expected MAExplorer names for the GIPO and quantification files,
additional database-specific pull-down menu plugins, names of gene
sets and sample condition lists, etc.
The GIPO file is independent of the number of array samples and
describes the mapping between spot position in an array and its gene
identification as well as corresponding data such as original plate
number, row and column; UniGene ID, GenBank ID, dbEST ID, etc. These
files will be described in more detail including how one can create
the necessary database files that MAExplorer requires for use with
various types of microarray data.
When running as a stand-alone application, MAExplorer assumes that
data from a local computer has a specific directory structure. The
required and optional directories (also called "folders" on some
operating systems) and files they contain are diagramed here from a
database project directory in your file system. The notation
"/folder-name" indicates that "folder-name" is a folder inside of the
project.
(specific database directories and files they contain)
/ Cache
/ (copies of any data files saved from Web DB access)
/ Config
/ MaExplorerConfig.txt
/ SamplesDB.txt
/ GIPO-db.txt
/ MAE
/ (set of startup database files).mae
/ Images
/ (set of original or sampled array .jpg images) (optional)
/ Plugins
/ (optional set of .jar or .class MAEPlugin files)
/ Quant
/ (set of spot quantified data files).quant
/ Report
/ (set of .txt and .gif report files generated using SaveAs
/ State
/ (set of gene set files).cbs and
/ (set of condition list files).hbl generated using Save DB
|
Figure C.1 Directory structure of stand-alone databases required by
MAExplorer. The "/Config", "/Quant", and "/MAE" directories are
required. The /MAE directory is only used with the stand-alone version
with .mae files, not
for the applet. [When used with an applet, the main path is the path
of the download JAR file and .mae files are not used.] The "/Report",
and "/State" directories are created by MAExplorer as needed and the
user need not create them prior to running MAExplorer. The text
reports and plot GIF images are saved in the /Report folder when you
"Save" a report or plot. When you "Save" the current database session
(File | Databases | Save ...), the gene sets and sample lists are
saved in the /State folder for use when you restart MAExplorer on the
.mae startup file. The optional "/Cache" directory is only used (and
then, only optionally) when downloading data from a Web server. The
optional "/Image" directory is only used in there are JPEG images of
the arrays provided and their resolution and alignment must correspond
to the (X,Y) spot data in the Quant files. The "/Plugins" directory is
where the
MAEPlugins packaged with MAExplorer are normally kept and where
MAExplorer looks when you attempt to load a plugin. Since you can
browse your file system, they do not have to appear here.
These could be used as examples that could be used in creating your
own database files. When the MAExplorer converter tool, Cvt2Mae, is
released it will eliminate the need for manually editing your database
files.
Sample MGAP database configuration, quantification data and startup
files are available for use as examples with which to make your own
files or for inspection.
In addition, examples of the (Config/, Quant/ and MAE/) files
needed for various types of arrays are available at:
When running MAExplorer as a stand-alone application, you may save
data on the disk Text reports and plot graphics windows are saved as
".txt" text and ".gif" image files when the user uses the "SaveAs"
button in the respective popup windows. These files are saved in the
"Report" subdirectory.
Similarly, when the entire database is saved (File | Databases |
SaveAs ...DB) into a .mae startup file, the set of gene set files are
saved as ".cbs" files and the set of condition list files are saved as
".hbl" files in the "State" subdirectory. These are automatically
reloaded into MAExplorer when the .mae startup file is used to restart
MAExplorer.
If your array data has JPEG or similar images of the original arrays,
the should be saved in the "Images" directory. For example, the
NCI-CIT mAdb database server allows you to download sampled images for
your data in an "Images" subdirectory at the same time you download
the other MAExplorer data files. The images can then be used by
various MAEPlugin programs. If your quantified data converted to
.quant files has (X,Y) coordinates corresponding to spots in these
images, then you may be able to use the Montage MAEPlugin to show
where the current spots are in sub-regions of all of the input
images. This plugin will be available on the MAEPlugin Web site when
we release the MAEPlugin facility for Beta-testing.
Software tools for aiding the construction of local stand-alone
databases from vendor supplied GIPOs and spot quantification files are
not available at this time, but will be made available in the future.
Manually constructing a local stand-alone database
Although the Cvt2Mae converter tool can convert many files, you could
alternatively build these files manually. We suggest using Excel or
your favorite RDBMS system to manipulate the data. At the end, save
the data into files with tab-delimited fields with the above file
extensions (i.e. .txt, .quant, .mae). The layout of these files and
what is optional and what is not is described in detail (maybe too
much!) below. You could use an ASCII file text editor instead of Excel
(such as Wordpad, Emacs, etc.) - but be careful not to add or
delete tabs since this will destroy the integrity of the database
tables. Be consistent in your file names; avoid spaces; use ASCII
characters in file names that are system independent (i.e. A-Z,
a-z,0-9, "-", "+", "_"); Use either "-" or "_" or both.
For a specific database (db), make sure the names of the configuration
files in /Config directory are entered in the
MaExplorerConfig-db.txt file for that database. You may have multiple
databases in the same /Config, /Quant and
/MAE directories if the file names do not conflict. The trick
is to have the .mae startup file in the /MAE
directory point to the specific configFile to be used. Since
MAExplorer reads the MaExplorerConfig-db.txt file when it first starts
up, it discovers the names of the other database files. If there is no
name conflicts, then there is no problem mixing data.
Each spot data (.quant) sample file has a name which must be entered
in the Database_File field of the Samples-db.txt row entry
for a new sample. The Sample_ID field is a descriptive name
of that sample.
Often GIPO files supplied by array vendors have additional fields not
currently used by MAExplorer. You can leave them in (they will be
ignored) or take them out (loading a database is faster).
If the field headings in the various user's tables are not the same
as that required by MAExplorer, you can easily fix this by adding
(Table,Field) mapping entries to your version of the
MaExplorerConfig-db.txt file (see mapTF
for examples).
Note that the optional Menu_Source_Name entry in the
Samples-db.txt file specifies the sub-menu, if any, that the sample
will appear in the Samples menu By Source sub-menu.
If the optional extra sample information file is used, then make sure
the sample names and database file names are the same, and that there
are corresponding rows in each table.
Quantified spot data from images scanned from hybridized sample arrays
may be created using a variety of software programs. Discussion of
these is beyond the scope of this manual. However, several of these
including Pathways 2.01, ImageQuant-NT, and others generate
tab-delimited text files. These files may be used directly as the
quantified spot files required by MAExplorer, or simplified first (by
removing unused or redundant data fields). Typically, the files are
named (or renamed) to that of the sample to distinguish them from each
other and a .quant file extension assigned instead of the
.txt file extension. Other programs generate tab-delimited
files that could be mapped to our .quant file formats. (For example,
the NCI/CIT mAdb system
generates such a mapping for GenePix(TM), and ScanArray
formated data.)
The following tables list parameters and some typical values
that might be included in the configuration and quantification files.
These examples illustrate the variety of parameters or fields with
examples of values that might be used. Required parameters are
in black with "(req)" prefix. Optional parameters are
indicated in blue with a "(opt)"
prefix. Optional parameters are not normally specified and are
generated in the .mae file when you save the state of a data
exploration. Parameters that might be used with Cy3/Cy5 ratio data
are indicated in magenta with a "(ratio)"
prefix. Future options not currently used are indicated in
green with a "(future)" prefix. Alternative
options are indicated in red with an "(alt)"
prefix.
The samples available to be analyzed in a database are listed in a
samples database table. This lists all samples that
could be loaded. The user will then select a subset of these to
be analyzed. The selection is done either in preset Web startup pages,
or with the stand-alone application .mae startup files, or at
run-time by selecting new entries from the Samples pull-down
menus. Extra information may be provided to MAExplorer for each sample
through this table and will be available for the Sample Array report in
Section 2.4.6.1.
A typical sample database table might look like:
Sample_ID Project Database_File
control 1 breastCancer control1
control 2 breastCancer control2
control 3 breastCancer control3
tumor 1 breastCancer tumor1
tumor 2 breastCancer tumor2
tumor 3 breastCancer tumor3
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You may optionally include a Database_ID field. For example:
Sample_ID Project Database_File Database_ID
control 1 breastCancer control1 270314
control 2 breastCancer control2 270315
control 3 breastCancer control3 270316
tumor 1 breastCancer tumor1 270317
tumor 2 breastCancer tumor2 270318
tumor 3 breastCancer tumor3 270319
|
The Database_ID may be useful if there are file length problems on
some systems (i.e. MacOS 8-9), we offer the option of using the
Database_ID as the file name for the .quant (Quant/ directory) and
.jpg (Images/ directory) rather than the Database_File name. For
example one could specify "Quant/270314.quant" and
"/Images/270314.quant" rather than the default "Quant/control1.quant"
and "/Images/control1.quant" names.
The Samples database table includes some required as well as optional
fields (see Table C.2.1.1):
Table C.2.1 List of Samples data file table fields. The Samples table
lists hybridized samples that are accessible to the user and
may be loaded into a database session if they wish.
(See Section C.1.1 for option notation.)
| Field |
Description |
| (req) Sample_ID |
descriptive name of the sample, free text.
[Note: an older depricated name is "Membrane_ID"] |
| (req) Project |
that the sample belongs. Used for login protection
and grouping of samples |
| (req) Database_File |
name of the .quant spot database file,
no spaces. This is the file name for the sample.
|
| (opt) DatabaseFileID |
database file ID corresponding to Database_File
and Sample_ID. For use with RDBMS Web databases (e.g. experiment id #).
NOTE: if you are encoding auxillary data files using this identifier,
e.g. sampled array images in the Images/ directory, then this field
is required if you want to access those images.
|
Table C.2.1.1 List of optional Samples data file table fields.
These fields may be used for some additional operations. If they are
not in the Samples DB table, then the operations will not be
available.
(See Section C.1.1 for option notation.)
| (opt) Menu_Source_Name |
Sample SubMenu j that this sample belongs.
You could use the word "Default" or leave out this entry if you do not
want to use sub menus. |
| (opt)Orig_File_Name |
if applicable. The original file name and sample name
if the data was split out from a multiple hybridized sample file. |
| (opt)Strain |
if applicable |
| (opt) Source |
if applicable |
| (opt) Probe |
if applicable |
| (opt) Stage |
if applicable (eg, developmental stage, dose,
time point, etc) |
| (opt) Login |
(optional) TRUE if login required with a Web server
else blank. This is used primarily with the Applet when interacting
with a Web server |
| (opt) GeneCard_URL |
GeneCard ID if applicable |
| (opt) Histology_URL |
(e.g. MGAP) histology DB Web page if applicable
|
| (opt) Model_URL |
(e.g. MGAP) mouse model database Web page if applicable |
| (opt) BGLow |
global low value of array background intensity |
| (opt) BGAvg |
global average value of array background intensity |
| (opt) BGRms |
global root-mean-square value of array background intensity |
Table C.2.1.2 List of optional Samples data file table fields.
These fields are not currently used in any computations but are
returned in the Sample Array
report in Section 2.4.6.1.
| (opt) Contributor |
name of researcher submitting the sample
|
| (opt) Contrib_Institute |
researcher's organization |
| (opt) Submission_Date |
when submitted |
| (opt) Exposure |
minutes or hours of radiolabel or fluorescent
exposure |
| (opt) Sample_Nbr |
internal sample number |
| (opt) FilterType |
name of the array layout |
| (opt) FilterType_Description |
additional description of array layout
|
| (opt) Comments |
details describing sample |
| (opt) Researcher |
researcher performing the hybridization |
| (opt) SampleGrid |
serial number of the array or grid or internal
laboratory numbering. (Useful if reusing arrays etc) |
MAExplorer has been designed to be able to read quantified spot data
from a variety of spot analysis software packages. So the data file
format is very flexible. Essentially, a data file contains one or
more spot intensity values per gene in each row of the data file. A
spot location is specified by a GIPO (field#, grid#, grid column#,
grid row#) 4-tuple with the field value optional. Note: a "grid" is
sometimes called a "block" or a "patch". If the field specification is
omitted and there are duplicate spots in multiple fields of grids,
then it is defined implicitly. In that case, the corresponding spot
intensity data for each field for a gene is specified as separate
columns going from left to right. The (grid#, column#, row#) part of
the specification may be encoded several ways: a) explicitly as
(grid#, column#, row#) or b) NAME_GRC.
Most quantitative data formats use integers for (grid,row,col)
values. However, some formats use letters [A:Z] for the first 26
(i.e. [1:26]), and [a:z] for the next 26 (i.e. [27:52])
values. Sometimes only lower case letters are used - in which case we
must map [a:z] to [1:26]. When MAExplorer first sees a letter in
reading the data, it checks to see if it is an upper or lowercase
letter and generates the offset needed to generate the mapping.
Alternatively, the Molecular Dynamics ImageQuant GIPO coordinates
represented by NAME_GRC with entries of the form "Grid
-<grid#>R<row#>C<column#>" (e.g. "Grid -3R6C8") may
be used with or without the replicated field entry to replace the
entries (grid, grid col, grid row) in the GIPO table and Quant spot
data files. For [G grids, R rows and C columns], this would cover a set
of spots in the range [1,1,1] through [G,R,C].
Some examples of typical quantified spot data files might look like:
- Single spot/gene intensity data.
grid grid col grid row RawIntensity Background
1 1 1 2226.8 32.6
1 1 2 1234.8 25.6
. . .
10 25 28 3333.8 23.6
- Double spots/gene intensity data contained in two fields of duplicate spots.
grid grid col grid row RawIntensity1 Background1 RawIntensity2 Background2
1 1 1 2226.8 32.6 2345.9 39.4
1 1 2 1234.8 25.6 1245.9 39.4
. . .
10 25 28 3333.8 23.6 3345.9 25.4
- Double spots/gene intensity data contained in two fields of duplicate spots.
field grid grid col grid row RawIntensity Background
1 1 1 1 2226.8 32.6
1 1 1 2 1234.8 25.6
. . .
1 10 25 28 3333.8 23.6
. . .
2 1 1 1 2226.8 39.4
2 1 1 2 1234.8 39.4
. . .
2 10 25 28 3333.8 25.4
- Double spots/gene intensity data using the Molecular Dynamics' NAME_GRC notation.
NAME_GRC RawIntensity1 RawIntensity2
GRID- 1-R1C1 2126.500 3662.350
GRID- 1-R2C1 2311.430 3306.290
GRID- 1-R3C1 3696.470 5780.310
GRID- 1-R4C1 3167.450 5245.440
. . .
- Cy3/Cy5 spot/gene ratio data.
grid grid col grid row Cy3 Cy3Bkgd Cy5 Cy5Bkgd
1 1 1 2226.8 32.6 2345.9 39.4
1 1 2 1234.8 25.6 1245.9 39.4
. . .
10 25 28 3333.8 23.6 3345.9 25.4
|
The basic Quant spot data file table includes entries listed in Table
C.3.1:
Table C.3.1 List of Quant data file table fields. This specifies the
spot quantification data. There may be one or more spots, corresponding
to the same gene, on each row.
(See Section C.1.1 for option notation.)
| Field |
Description |
| (opt) field |
field for duplicate genes if using single
'RawIntensity' value/Row |
| (req) grid |
grid name (either A,B,C,... or 1,2,3,... ) |
| (req) grid col |
column with in a grid |
| (req) grid row |
row within a grid |
| (opt+alt) NAME_GRC |
(alternative specification of "grid, grid col, grid row"). |
| (req) RawIntensity1 |
intensity value for field 1. Use this form if there
is more than 1 intensity value/row. |
| (req) RawIntensity2 |
intensity value for field 2
(required if it exists and for Cy3, Cy5 data)
|
| (req+alt) RawIntensity |
intensity value for field 1,
if only one field used |
| (opt) Background1 |
background intensity value for field 1 |
| (opt) Background2 |
background intensity value for field 2
(if it exists for F1,F2 data or Cy3, Cy5 data)
|
| (opt+alt) Background |
background intensity value for field 1,
if only one field used |
| (opt) QualCheck |
quality check for data
indicating "bad" spots or genes. Current codes are
listed in the Table C.4.2 of QualCheck semantics |
| (opt) DetValue |
spot data detection value quality. This could
be the Affymetrix MAS5.0 "Detection p-value" or some other metric
correlated with spot detection quality in the range of [0.0 : 1.0].
metrix
|
Note: If NAME_GRC is specified (eg. for use with ImageQuant-NT data),
then the explicit (grid, grow row, grid col) fields are not
required. Note: For [G grids, R rows and C columns], this would cover
a set of spots in the range [1,1,1] through [G,R,C].
Note: If Cy3/Cy5 double fluorescent labeling is used, then the
RawIntensity1 and RawIntensity2 fields may be replaced with Cy3RI and
Cy5RI names and the (RawIntensity1, RawIntensity2) fields mapped to
(Cy3RI, Cy5RI) in the configuration file mapTF entries (table C.5.4 below).
(See Section C.1.1 for option notation.)
| Field |
Description |
| (req) Cy3RI |
RawIntensity1 value for Cy3 |
| (req) Cy5RI |
RawIntensity2 value for Cy5 |
| (opt) Cy3Bkgrd |
Background1 value for Cy3 |
| (opt) Cy5Bkgrd |
Background2 value for Cy5 |
| (opt) Cy3 |
RawIntensity1 value for Cy3 |
| (opt) Cy5 |
RawIntensity2 value for Cy5 |
C.4 The GIPO table database file format
The gene-in-plate-order (GIPO) table used to make the connection
between a spot on a microarray and the plate well corresponding to a
gene. We are working on extending the format so that it will more
easily handle GIPO tables from a variety of sources.
Data is extracted from a table created from the gene-in-plate-order
(GIPO) gene coordinate table. This links spots in a microarray to
these Genomic "gene ID"s and gene names. This table may contain
Clone ID, GenBank, dbEST, UniGene IDs, LocusID corresponding to these
Master Gene IDs. An optional table of Clone IDs and Gene Classes the gene
belongs to may also be defined.
A typical GIPO database table might look like:
Location grid grid col grid row plate plate row plate col Clone ID GenBankAcc GeneName
. . .
39 A 2 15 2 1 3 1247601 AA763423 "Mus musculus A kinase anchor protein (AKAP-KL) mRNA, alternatively spliced isoform 1, complete cds"
40 A 2 16 2 1 4 1247553 AA763380 Mus musculus bodenin gene
41 A 2 17 2 1 5 1247865 AI465019 "Mouse beta-D-galactosidase fusion protein mRNA, complete cds"
. . .
|
The basic GIPO table includes the following fields:
Table C.4 List of GIPO data file table fields.
These fields define the mapping between a spot's grid coordinates on
the array and its genomic identifier, gene name, its plate, etc.
| Field |
Description |
| (opt) field |
array field for duplicate genes |
| grid |
array grid name (either A,B,C,... or 1,2,3,... ) |
| grid col |
array column within a grid (either A,B,C,... or 1,2,3,... ) |
| grid row |
array row within a grid (either A,B,C,... or 1,2,3,... ) |
| (opt+alt) NAME_GRC |
alternative specification to "grid, grid col, grid row".
It is generated by the Molecular Dynamics spot quantification software.
|
| (opt) Master Gene ID |
This is the master gene identifier
used in MAExplorer. It must be one or more of the identifiers listed
in Table C.4.3. One of
these will be selected as the Master Gene ID (MID)
|
| (req) Gene Name |
Master Gene Name.
The GeneName options are listed in Table C.4.1. These alternative
GeneClasses are automatically
recognized from the Gene Name. |
| (opt) plate |
plate name for original gene. If this
is not specified, it uses the grid value. |
| (opt) plate row |
plate row name for original gene. If this
is not specified, it uses the grid row value. |
| (opt) plate col |
plate column name for original gene. If this
is not specified, it uses the grid col value. |
| (opt) QualCheck |
quality check for data indicating "bad" spots or
genes. Current codes are listed in the Table C.4.2
below |
Table C.4.1 List of possible Master Gene Name
The Master Gene Name must be define as one the following identifiers:
| Field |
Description |
| (opt) GeneName |
Gene name |
| (opt) Unigene cluster Name |
alternative for GeneName if the latter is
not specified. |
Some Gene Classes are automatically recognized from
the Gene Name including:
- Unknown ESTs - the Gene Name is "EST", "ESTs", "expressed sequence",
"unknown"
- ESTs similar to known genes - the Gene Name is "EST, ...",
"EST ...", "expressed sequence ..."
- Calibration DNA - the Gene Name is the 'calibDNAname' value
defined in the Configuration database table.
- User's Plates - the Gene Name is the 'your plate' value defined in
the Configuration database table.
- Empty Well - the Gene Name is the 'EmptyWell' value defined in
the Configuration database table.
- Known genes - if the non-null Gene Name does not fit into any of
the above categories and it is not an empty well, it is assumed to be
a known gene.
- Good genes - normally set by the QualCheck field in the GIPO file, but
if the gene name is "EmptyWell", it is flagged as a bad gene.
Some quantification programs (e.g. Molecular Dynamics "ImageQuant-NT) specify
"grid, grid_col, grid_row" by a single symbol we denote NAME_GRC coded
as follows
GRID- grid#-Rrow#Ccol#
For example, if grid #, row# and column# are (8,12,11), then it codes it as
GRID- 8-R12C11
Table C.4.2 List of QualCheck codes and their semantics
The data filter "Filter by 'Good Spot data'" may be used in
eliminating bad spot data on a per-gene set basis. This uses the
"QualCheck" field in the quantified data table is present. It maps
either an 1) integer numeric code (see Appendix C of the Reference
Manual), 2) an alphabetic code (e.g. Affymetrix "Abs Call") of "P" (or
"G" or "T") to Good Spot, "A" (or "B" or "F") to Bad Spot, and "M" to
Marginal Spot, or 3) a continuous quality value. In this latter case,
QualCheck may be a continuous monotonically increasing floating point
value (e.g. 0.0 to 100.0, or 0.0 to 1.0, -100.0 to +100.0, etc.) in which case a "Spot
Quality" State threshold slider will popup when the filter is invoked.
Additional property value codes may be added in the future.
| Status |
QualCheck value |
Semantics |
| Good gene |
2 |
the spot data is "Good" (some systems
report this by a NULL quality measure). It has a good gene name.
Alternatively, letter codes may be used "P", "G", "T".
|
| Bad gene |
4 |
the spot data is bad, a good gene name.
|
| Bad spot |
8 |
is a non-analyzable spot (eg. marker, or "Bad", "Not Found",
"Empty". etc.) Alternatively, letter codes may be used "A", "B", "F".
|
| Duplicate spot |
16 |
is duplicate of another gene on array |
| Marginal spot |
256 |
is a marginally quantified spot.
Alternatively, letter codes may be used "M".
|
Table C.4.3 List of possible Master Gene Identifiers
Additional data is used to point to data in external genomic databases
by specifying the identifier. This may be used to dynamically link
genes in the MAExplorer database to Web database servers to bring up
Web pages from these databases. Note the Master ID needs to be
specified and may be any one of the following identifiers. The
appropriate genomic Web browser access will be enabled depending on
the genomic Master ID specified.
(See Section C.1.1 for option notation.)
The fields include:
| Field |
Description |
| (opt) Location |
alternate spot identifier. E.g., Affymetrix 'probe_set', or
Incyte 'IncyteID', etc. This may be numeric or alphanumeric
|
| (opt) Clone ID |
I.M.A.G.E. consortium database clone ID. It may have a
"IMAGE:" or "ATCC:" prefix |
| (opt) Unigene cluster ID |
NCBI UniGene database ID |
| (opt) dbEST3' |
NCBI dbEST database |
| (opt) dbEST5' |
NCBI dbEST database |
| (opt) GenBankId |
NCBI GenBank database |
| (opt) GenBankId3' |
NCBI GenBank database |
| (opt) GenBankId5' |
NCBI GenBank database |
| (opt) RefSeqID |
NCBI RefSeq database |
| (opt) LocusID |
NCBI LocusLink database |
| (opt) OMIMID |
NCBI OMIM database |
| (opt) SwissProtID |
Swiss-Prot database |
Table C.4.4 Extending Genomic IDs and associated URLs
MAExplorer allows you to define your own gene identifiers that will
map to external genomic databases. You add the following entires in
sets of 4 to the Configuration database or to the .mae startup file.
These entries will be added to the View menu where you may select the
external genomic database to visit when you activate MAExplorer to
launch a brower on clicking on a gene. The following table shows the 4
required fields for 2 entries. There may be any number of external
genomic IDs.
(See Section C.1.1 for option notation.)
| Parameter |
Value |
DataType |
Comments |
| (opt) GenomicMenu1 |
GenBank |
String |
Name of the database. This will appear in the View menu |
| (opt) GenomicURL1 |
http://www.ncbi.nlm.nih.gov/htbin-post/Entrez/query?db=2&form=1&term=
|
String |
URL to which one adds the 'GenomicIDreq' value |
| (opt) GenomicURLepilogue1 |
|
String |
epilogue of the URL if any |
| (opt) GenomicIDreq1 |
GBID |
String |
Name of the GenomicID required and that is specified
in the GIPO file as one of its fields |
| (opt) GenomicMenu2 |
UniGene |
String |
Name of the database. This will appear in the View menu |
| (opt) GenomicURL2 |
http://www.ncbi.nlm.nih.gov/UniGene/query.cgi?ORG=Mm&CID=
|
String |
URL to which one adds the 'GenomicIDreq' value |
| (opt) GenomicURLepilogue2 |
|
String |
epilogue of the URL if any |
| (opt) GenomicIDreq2 |
UID |
String |
Name of the GenomicID required and that is specified
in the GIPO file as one of its fields |
C.5 Configuring MAExplorer for use with various types of array data
MAExplorer has been designed so that it may be reconfigured for
different array dependencies including: geometries, number of replicate
fields, scanner dynamic ranges, labeling, etc. When first started,
MAExplorer reads this configuration file and then uses this
information to handle reading different types of array data files that
are subsequently loaded. To make it easier to understand, the entire
table is presented as several sub-tables - however, MAExplorer reads
it as a single table (the default being called
MaExplorerConfig.txt). Note that optional parameters are
for the most part - optional. Many of these may be set from the
MAExplorer menus once the program is started. The reconfigured
state may then be saved (File | Database | SaveAs ... DB) with
these and other state values retained for the next time the particular
startup database is used.
We are developing tools for creating and editing the configuration
file. In the mean time, edit the file with Excel and save the finished
table as a tab-delimited text file with the name
MaExplorerConfig.txt in the Config sub-directory) in
the directory where your database is stored.
Table C.5 List of Configuration data file table fields.
| Parameter subset |
Function of these parameters |
|---|
| 1. Array content & geometry |
Describes the content and geometry of the arrays (required) |
| 2. Threshold defaults |
Describes the threshold defaults (optional) |
| 3. Array database files |
Describes the array specific database files (required) |
| 4. Table field mapping |
Describes "mapTF" table,field mapping. This maps user defined names
to names required by MAExplorer and is only required if the user names
are different from the names MAExplorer expects. |
| 5. URL genomic databases |
Describes base addresses of genomic Web DBs (optional).
If you do not specify these, default values are supplied from
the program. |
| 6. User menus |
Describes user-specific menus (optional) |
The following sub-tables list the configuration parameters and
some typical values that might be included. These examples illustrate
the variety of parameter options with examples of values that
might be used. Required entries are listed at the tops of the tables.
A typical MAExplorer minimal configuration database table might look
like:
Parameter Value DataType Comments
MAX_FIELDS 1 int # replicate grids/array
MAX_GRIDS 2 int # grids/field
MAX_GRID_COLS 38 int # columns/grid
MAX_GRID_ROWS 27 int # rows/grid
usePseudoXYcoords true boolean use pseudoarray XY coord image - no XY data
gipoFile GIPO.txt File name of GIPO file from
samplesDBfile SamplesDB.txt File name of Samples DB file
dataBase demo String default name of project database
dbSubset demo1 String default database subset name
useRatioData true boolean treat duplicate(F1,F2) data as ratio (F1/F2) - i.e.Cy3/Cy5
EditDate Tue Aug 21 2000 String demo
|
Table C.5.1 List of array database-specific content and
geometry configuration (Parameter,Value) entries
This table lists most of the options that the use could define. If
they define an option, it will override the default set by
MAExplorer. The values are shown for some typical databases. (See (A
HREF="#optTblNotation">Section C.1.1 for option notation.)
A) Array geometry parameters
| Parameter |
Value |
DataType |
Comments |
| (req) MAX_FIELDS |
2 |
int |
# duplicate grids (blocks, patch, etc.) of spots for
each gene in the array (i.e. F1, F2, etc.). Note that Cy3 and Cy5 data
for each spot count as one field. |
| (req) MAX_GRID_COLS |
24 |
int |
# cols/grid in the array |
| (req) MAX_GRID_ROWS |
9 |
int |
# rows/grid in the array |
| (req) MAX_GRIDS |
8 |
int |
# grids in the array |
| (opt) ignoreExtraFields |
FALSE |
boolean |
if there are additional fields of data in the
GIPO or .quant files, then ignore them. Only use the first rawIntensity
field. Note: this option is not normally used.
|
| (opt) reuseXYcoords |
FALSE |
boolean |
Reuse XY coordinates from first sample
for rest of the samples |
| (opt) SpotRadius |
7 |
int |
(2 to 20 pixels) 50 microns, scroller.
Note: this should be set to about 4 or 5 for a 10000 gene DB.
|
| (opt) swapRowsColumns |
FALSE |
boolean |
set if swap rows and columns in the array
(used with our particular Research Genetics arrays) |
| (opt) usePseudoXYcoords |
FALSE |
boolean |
use pseudoarray XY coordinates image if there is no
explicit no XY spot position data generated by the quantification
software |
| (future) FIELD_LAYOUT |
LtoR |
String |
fields are Left to Right |
| (future) FIELDS_ARE_NUMBERED |
TRUE |
boolean |
Data files contain field number.
Otherwise field is extrapolated |
| (future) GRID_LAYOUT |
Horizontal |
String |
Grids are Left To Right in the array |
| (future) GRID_PER_ROW |
4 |
int |
# grids per row in each field of the array |
B) Ratio and background parameters
| Parameter |
Value |
DataType |
Comments |
| (ratio) fluorescentLbl1 |
Cy3 |
String |
name of dye for fluorescent label 1 |
| (ratio) fluorescentLbl2 |
Cy5 |
String |
name of dye for fluorescent label 2 |
| (ratio) useRatioData |
TRUE |
boolean |
set if data is Cy3/Cy5 ratio data otherwise
it assumes intensity data for each spot |
| (opt+ratio) useRatioMedianCorrection |
FALSE |
boolean |
when using ratio data mode (Cy3/Cy5),
use ratio median correction as the default |
| (opt) useBackgroundCorrection |
FALSE |
boolean |
use background correction as the default when startup |
| (future) useCy5/Cy3 |
FALSE |
boolean |
compute Cy5/Cy3 ratios instead of Cy3/Cy5 ratios |
C) Names of database, etc.
We indicate example values by italics.
| Parameter |
Value |
DataType |
Comments |
| (opt) calibDNAname |
mouse genomic DNA |
String |
name for calibration DNA if available - replacing
cloneID in the case where the clones are not yet in the I.M.A.G.E.
database. The particular clone is located using the Plate(grid,row,col)
reported when selecting the current gene.
|
| (opt) classNameX |
HP-X 'set' |
String |
default name of HP-X samples 'set' |
| (opt) classNameY |
HP-Y 'set' |
String |
default name of HP-Y samples 'set' |
| (opt) dataBase |
MGAP DB |
String |
name of the database project |
| (opt) dbSubset |
Preg 13 vs Lact 1 |
String |
name of the subset of data from the database |
| (opt) geoPlatformID |
GPL80 |
String |
name of the NCBI Gene Expression Omnibus (GEO) Platform Id |
| (opt) maAnalysisProgram |
Research Genetics Pathways 2.01 |
String |
name of spot quantification program |
| (opt) yourPlateName |
your plate |
String |
name of researcher's clones if available - used in the
cloneID data field in the case where the clones are not yet in the I.M.A.G.E.
database. The particular clone is located using the Plate(grid,row,col)
reported when selecting the current gene.
(See Table 2.4.1)
|
| (opt) emptyWellName |
empty wells |
String |
what you called empty wells if there are any in the
database.
(See Table 2.4.1)
|
| (opt) EditDate |
06-19-00, Lemkin |
String |
comment why changed |
D) Display Views
| Parameter |
Value |
DataType |
Comments |
| (opt) gangSpotFlag |
TRUE |
boolean |
set gang spot display on startup for database
with duplicate spots |
| (opt) presentationViewFlag |
FALSE |
boolean |
start MAExplorer with larger fonts and graphics
symbols suitable for live presentations |
| (opt) showEGLflag |
FALSE |
boolean |
show EGL genes on startup from previously saved
database that had EGL genes selected. |
| (opt) showMouseOver |
TRUE |
boolean |
show mouse-over info when move mouse in windows |
| (opt) useDichromasy |
FALSE |
boolean |
use orange-blue else use red-green color scheme |
| (opt) viewFilteredSpotsFlag |
TRUE |
boolean |
view Filtered spots the array pseudoimage. If it is
off, it shows just the pseudoarray image without spots passing the
filter or MAExplorer state information. |
Note that there are many other parameters reflecting the state of
MAExplorer that are saved in the .mae startup file when doing a (File
| Database | SaveAs...DB) operation. These are reviewed and set from
the MAExplorer menus. These parameters are not listed here - although
they could be used in setting up an initial .mae startup file.
Table C.5.2 List of default threshold database-specific
configuration (Parameter,Value) entries
Some of the default thresholds and sizes may be defined here as
it may be useful to vary them with different types of data.
| Parameter |
Value |
DataType |
Comments |
| (opt) CanvasHorSize |
1100 |
int |
pixels, horizontal size of microarray image **DEPRICATED**
|
| (opt) CanvasVertSize |
1100 |
int |
pixels, vertical size of microarray image **DEPRICATED**
|
| (opt) fontFamily |
SansSerif |
String |
default text font family. See Font Family for
other fonts. Some fonts look better with some operating systems. |
| (opt) clusterDistThr |
10 |
float |
default cluster similarity threshold in
[0.0 : 100.0], scroller |
| (opt) maxGenesReported |
50 |
int |
max # of genes in highest/lowest gene
report |
| (opt) maxPreloadImages |
4 |
int |
max # HP samples to initially load |
| (opt) nbrOfClustersThr |
6 |
int |
default # clusters for K-means clustering |
| (opt) pValueThr |
0.2 |
float |
default p-value for statistical tests |
| (opt) spotCVthr |
0.25 |
float |
default spot Coefficient of Variation value |
| (opt) allowNegQuantDataFlag |
FALSE |
boolean |
set if .quant file data has negative intensity values
otherwise it clips the negative values to 0.0 |
| (opt) usePosQuantDataFlag |
TRUE |
boolean |
Filter out genes where .quant file data has negative
intensity values otherwise it uses the negative data |
Table C.5.3 List of array specific auxiliary database files
(Parameter,Value) entries
This lists the names of the database-specific auxiliary files. Note
that the names of these files may change with the database but the
name of the initial configuration file containing these names (i.e.
MaExplorerConfig.txt does not change. Optional Parameters
are indicated with a "*" prefix.
(See Section C.1.1 for option notation.)
| Parameter |
Value |
DataType |
Comments |
| (req) gipoFile |
GIPO-DB.txt |
File |
Composite Gene-In-Plate-Order (GIPO) file
containing the spot print order, Clone-IDs, gene names, GenBank
IDs, plate coordinates, etc.
(See Appendix C.4)
|
| (req) samplesDBfile |
Samples-DB.txt |
File |
list of hybridized samples in the database. [Note:
an older depricated name was "membranesDBfile"].
(See Appendix C.2)
|
| (opt) quantFileExt |
.quant |
String |
alternate quantification spot file name extension
to use instead of ".quant". (You might set it to ".txt")
(See Appendix C.3)
|
Table C.5.4 List of optional (Table,Field) mappings to
configure specific user's data types
Sometimes user data tables contain the proper data required by
MAExplorer, but the names of the columns (i.e. fields) are
different. MAExplorer can map user (table,field) names to the internal
names it uses. This allows users to maintain their tables in the names
they choose. The following mapTF entries are not required if
the fields in the corresponding tables already have the MAE field
name. The entries use the mapping where
- [TableName] is the name of the table (repeated twice in the
following specification).
- [MAE field name] is the internal MAExplorer name of the
field in the table.
- [User field name] is the external name of the field in table in
the user's file that corresponds to the internal MAExplorer
field.
[TableName],[MAE field name],[TableName],[User field name]
The following table fields may be mapped. Note: mapping is
required only when the table field names of your data files are
different than the internal MAExplorer table field names.
- GipoTable - GIPO table for entire database
- SamplesTable - list of all samples in the database
- QuantTable - each .quant spot data file
The following is an example of some of the parameters that might be
added to the Configuration file to perform field name mappings. Note:
these mappings are only required if the data field names are non-standard.
This shows some typical field name mappings. It will not be the same
for your data.
(See Section C.1.1 for option notation.)
| Parameter |
Value |
DataType |
Comments |
| (opt) mapTF |
GipoTable,grid,GipoTable,SA |
String |
GIPO table grid name (numbers or letters) |
| (opt) mapTF |
GipoTable,grid row,GipoTable,R |
String |
GIPO table row of grid name (numbers or letters) |
| (opt) mapTF |
GipoTable,grid col,GipoTable,C |
String |
GIPO table column of grid name (numbers or letters) |
| (opt) mapTF |
GipoTable,plate,GipoTable,RG Pl |
String |
GIPO table plate where clone came from |
| (opt) mapTF |
GipoTable,plate row,GipoTable,RG row |
String |
GIPO table row of plate where clone came from |
| (opt) mapTF |
GipoTable,plate col,GipoTable,RG col |
String |
GIPO table column of plate where clone came from |
| (opt) mapTF |
GipoTable,Clone ID,GipoTable,Clone id |
String |
GIPO name of Clone ID |
| (opt) mapTF |
GipoTable,GeneName,GipoTable,Gene name |
String |
GIPO table map gene name |
| (opt) mapTF |
GipoTable,Unigene cluster ID,GipoTable,ucid |
String |
GIPO table UniGene cluster id (if available) |
| (opt) mapTF |
Unigene cluster name,GipoTable,ucn |
String |
GIPO table UniGene cluster name (if available) |
| (opt) mapTF |
GipoTable,GenBank 3',GipoTable,gb3' |
String |
GIPO table GenBank 3' id (if available) |
| (opt) mapTF |
GipoTable,GenBank 5',GipoTable,gb5' |
String |
GIPO table GenBank 5' id (if available) |
| (opt) mapTF |
GipoTable,dbEST 3',GipoTable,est3' |
String |
GIPO table dbEST 3' id (if available) |
| (opt) mapTF |
GipoTable,dbEST 5',GipoTable,est5' |
String |
GIPO table dbEST 5' id (if available) |
| (opt) mapTF |
QuantTable,grid,QuantTable,SA |
String |
Quant table array grid name (numbers or letters) |
| (opt) mapTF |
QuantTable,grid row,QuantTable,R |
String |
Quant table row of grid name (numbers or letters) |
| (opt) mapTF |
QuantTable,grid col,QuantTable,C |
String |
Quant table column of grid name (numbers or letters) |
| (opt) mapTF |
QuantTable,RawIntensity,QuantTable,Intensity |
String |
Quant table RawIntensity data |
| (opt) mapTF |
QuantTable,Background,QuantTable,BkgrdIntens |
String |
Quant table background intensity |
| (opt) mapTF |
QuantTable,RawIntensity1,QuantTable,Cy3RI |
String |
Quant table RawIntensity1 Cy3 data |
| (opt) mapTF |
QuantTable,RawIntensity2,QuantTable,Cy5RI |
String |
Quant table RawIntensity2 Cy5 data |
| (opt) mapTF |
QuantTable,Background1,QuantTable,BkgrdCy3RI |
String |
Quant table background intensity for Cy3 |
| (opt) mapTF |
QuantTable,Background2,QuantTable,BkgrdCy5RI |
String |
Quant table background intensity for Cy5 |
These entries are base addresses of genomic and other Web servers that
are used for accessing gene or hybridized sample specific data in
external databases. Note that these entries are hardwired in
MAExplorer and do not need to be specified in the Configuration file
unless you wish to override these defaults.
| Parameter |
Value |
DataType |
Comments |
| (opt) dbEstURL |
http://www.ncbi.nlm.nih.gov/irx/cgi-bin/birx_doc?
dbest+ |
String |
NCBI dbEst server by dbEST ID.
You may use an alternative server. |
| (opt) GenBankAccURL |
http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Search&db=Nucleotide&term=
|
String |
NCBI GenBank server by GenBankAcc ID.
You may use an alternative server. |
| (opt) GenBankCloneURL |
http://www.ncbi.nlm.nih.gov/irx/cgi-bin/submit_form_query?
TITLE=dbEST+Retrieval+Output&INPUTS=1&
BRACKETS=NONE&ADDFLAGS=-b&DB=dbest&
NDOCS=10&Q1= |
String |
NCBI GenBank entry by Clone_ID server.
You may use an alternative server. |
| (opt) GenBankCloneURLepilogue |
[clin] |
String |
Epilog added after Clone_ID.
You may use an alternative server. |
| (opt) IMAGE2GenBankURL |
http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?
ORG=Mm&ACC=IMAGE: |
String |
lookup GenBank from CloneID server.
You may use an alternative Image to GenBank server.
The "ORG=Mm" should be changed to reflect
the proper species, eg. "ORG=Hs" for human, etc. |
| (opt) IMAGE2GIDURL |
http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?
ORG=Mm&GID=IMAGE: |
String |
NCI/CIT lookup GenBank GID from CloneID server.
You may use an alternative CloneID to GenBank GID server.
The "ORG=Mm" should be changed to reflect
the proper species, eg. "ORG=Hs" for human, etc. |
| (opt) IMAGE2unigeneURL |
http://nciarray.nci.nih.gov/cgi-bin/UG_query.cgi?
ORG=Mm&CLONE=IMAGE: |
String |
NCI/CIT lookup UNIGENE from CloneID server.
You may use an alternative CloneID to UniGene server.
The "ORG=Mm" should be changed to reflect
the proper species, eg. "ORG=Hs" for human, etc. |
| (opt) unigeneURL |
http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?
ORG=Hs&CID=
|
String |
NCBI UNIGENE by Clone ID server.
You may use an alternative UniGene server.
The "ORG=Hs" should be changed to reflect
the proper species, eg. "ORG=Mm" for mouse, etc. |
| (opt) locusLinkURL |
http://www.ncbi.nlm.nih.gov/LocusLink/list.cgi?
SITE=104&V=1&ORG=Hs&ORG=Mm&ORG=Rn&ORG=Dr&ORG=Dm&Q=
|
String |
NCBI LocusLink by GenBank ID server.
The LocusLink server is accessed by LocusID |
| gbid2LocusLinkURL |
http://www.ncbi.nlm.nih.gov/LocusLink/list.cgi?SITE=104
&V=1&ORG=Hs&ORG=Mm&ORG=Rn&ORG=Dr&ORG=Dm&Q=
|
String |
NCBI LocusLink by LocusID server.
The LocusLink server is accessed by LocusID |
| (opt) swissProtURL |
http://www.expasy.ch/cgi-bin/get-sprot-entry? |
String |
SwissProt by SwissProt ID |
| (opt) omimURL |
http://www.ncbi.nlm.nih.gov:80/entrez/dispomim.cgi?id=
|
String |
NCBI OMIM database by OMIM ID |
| (opt) pirURL |
http://pir.georgetown.edu/cgi-bin/iproclass/iproclass?choice=entry&id=
|
String |
PIR ProClass database by SwissProt ID |
| (opt) GeneCardURL |
http://bioinfo.weizmann.ac.il/cards-bin/carddisp? |
String |
GeneCard DB server.
You may use an alternative server. |
| (opt) histologyURL |
http://mammary.nih.gov/models/ |
String |
E.g NIDDK MGAP histology DB server. If you have
an alternative histology model server, put it here. |
| (opt) modelsURL |
http://mammary.nih.gov/models/ |
String |
e.g. NIDDK MGAP mouse models DB server.
You may use an alternative models server. |
| (opt) proxyServer |
http://www.lecb.ncifcrf.gov/cgi-bin/maeProxySvr? |
String |
NCI/LECB proxy server to access servers outside of the
Java "sandbox". If you set up MAExplorer on your local server, then]
this should point to a proxy server on your system. |
When creating a specific MAExplorer database, the Help menu may be
configured for specific links to related databases. Any number of
additional Help entries may be used (including none). The following
shows the entries for MGAP.
| Parameter |
Value |
DataType |
Comments |
| (opt) HelpMenu1 |
List of hybridized samples |
String |
Help sub menu URL |
| (opt) HelpMenu2 |
MGAP animal models |
String |
Help sub menu URL |
| (opt) HelpMenu3 |
MGAP home page |
String |
Help sub menu URL |
| (opt) HelpURL1 |
http://www.lecb.ncifcrf.gov/mae/maeHybridizations.html |
String |
Help sub menu URL |
| (opt) HelpURL2 |
http://mammary.nih.gov/models/ |
String |
Help sub menu URL |
| (opt) HelpURL3 |
http://mammary.nih.gov/ |
String |
Help sub menu URL |
When creating a specific MAExplorer database, the Plugin menu entries
may be added to different parts of the menu tree. Any number of
additional unique Plugin entries may be used (including none). The following
table illustrates some possible plugin specifications that can be
loaded (or not) at startup time or loaded when invoked from a menu.
| Parameter |
Value |
DataType |
Comments |
| (opt) PluginMenuName1 |
New Cluster plot |
String |
Plugin sub menu string |
| (opt) PluginMenuStubName1 |
PlotMenu:cluster |
String |
name of Plugin menu stub to add menu entry |
| (opt) PluginClassFile1 |
NewClusterPlot.jar |
String |
Name of class file |
| (opt)sPluginCallAtStartup1 |
InstallInMenu |
String |
handling plugins at startup: "InstallInMenu", "RunOnStartup", "NoInstall" |
| (opt) PluginMenuName2 |
New sample report |
String |
Plugin sub menu string |
| (opt) PluginMenuStubName2 |
ReportMenu:sample |
String |
name of Plugin menu stub to add menu entry |
| (opt) PluginClassFile2 |
NewSampleReport.jar |
String |
Name of class file |
| (opt)sPluginCallAtStartup2 |
InstallInMenu |
String |
handling plugins at startup: "InstallInMenu", "RunOnStartup", "NoInstall" |
| (opt) PluginMenuName3 |
Client-server |
String |
Plugin sub menu string |
| (opt) PluginMenuStubName2 |
-none- |
String |
name of Plugin menu stub to add menu entry |
| (opt) PluginClassFile2 |
ClineServerMAE.class |
String |
Name of class file |
| (opt)sPluginCallAtStartup2 |
InstallInMenu |
String |
handling plugins at startup: "InstallInMenu", "RunOnStartup", "NoInstall" |
List of acceptable Menu stub names for: PluginMenuStubName
When MAEPlugin's are available, you will be able to insert them into various
parts of the MAExplorer menu. If the menu stub is not found, it will
install them in the generic "Plugin" pull-down menu.
- "FileMenu"
- "FileMenu:Databases"
- "FileMenu:State"
- "FileMenu:Groupware"
- "HPmenu"
- "GeneClassMenu"
- "NormMenu"
- "EditMenu"
- "EditMenu:EGL"
- "EditMenu:GeneSet"
- "EditMenu:CondList"
- "EditMenu:Preferences"
- "FilterMenu"
- "PlotMenu"
- "PlotMenu:EPplots"
- "PlotMenu:Histogram"
- "PlotMenu:PseudoArray"
- "PlotMenu:ScatterPlots"
- "ReportMenu"
- "ReportMenu:Genes"
- "ReportMenu:Samples"
- "ClusterMenu"
- "ClusterMenu:ClusterFlags"
- "ViewMenu"
- "PluginMenu"
- "HelpMenu"
C.6 Using the Cvt2Mae 'wizard' tool to convert your array
data for use with MAExplorer
In order to use MAExplorer on your data, you must convert your data
files into the data formats described in
Appendix C and Appendix D. Although
we and others have done this by editing user's data files into the
required formats, it is a non-trivial process.
Therefore we have created a Java conversion tool called Cvt2Mae to automate these
conversions. You may 
and install Cvt2Mae on your computer and use it to
convert your array data to MAExplorer data format. Figure C.6.1 shows
Cvt2Mae array data converter.
Cvt2Mae is a "Wizard" driven process designed for use by molecular
biologists. It handles commercial chips such as Incyte, Affymetrix,
GenePix, Scanalyze, etc. or one-of-a-kind academic chips. It asks you
questions to describe your chip and your data. We call the chip
description the "Array Layout". After you have created or edited an
array layout, you may save it for use in future conversions. [The
array layouts are kept in a subdirectory "ArrayLayout" in the
directory where you installed Cvt2Mae.] Since an ArrayLayout is a
file, you could mail it to a collaborator. After you have answered the
questions, you then run the converter and it generates the proper set
of converted data files. In the case of user defined array layouts,
we denote the latter as <User-defined> where the user assigns a
name to that layout as part of the description. Essentially, the array
layout contains a set of "rules" for describing the user's array data
so Cvt2Mae knows how to read it. At some point, we plan to add the
MAGE-ML standard to Cvt2Mae as one of the array layouts so it should
be able to handle a wider variety of data.
If your array geometry does not conform to one of those handled by
MAExplorer (see Section 1.1
Gene coordinate numbering on the microarray), then treat the data
as an list of spots. In Cvt2Mae Wizard panel "[2] Grid geometry data",
select the checkbox "Use # spots (BELOW), else grid-geometry (ABOVE)"
and then enter the total number of spots in the line below. This will
construct an arbitrary pseudoarray geometry to serve as a basis to
display the microarray pseudoimage (see the Algorithm for constructing
the pseudo array from a list of spots in Appendix C.6). For
example, this might be used in the case where your arrays used
meta-grids.
Figure C.6.1 The Cvt2Mae array data converter. Selecting a
Chipset Array Layout. The built-in array layouts are shown for the
various chip types. User-defined layouts may be added by selecting
the <User-defined> layout then editing the layout using the
Edit Layout, Assign GIPO fields, and Assign Quant fields. These options
are described in more detail in the Cvt2Mae home page..
Converting data for known chip "Array Layouts" or lists of quantified
spots
Assuming the desired array is in the list of chip array layouts,
follow the eight step process below with steps 3 and 5 omitted. If the user
must describe their own array data using the <User-defined> chip
array layout, then they would do step 3. If your chip is one of the
chips listed in the chip Array Layouts list, then you may be able to
do an "Edit Layout" to modify the description without having to define
the chip layout from scratch - in which case do step 3.
- Select the desired Array Layout.
- Select the set of input files to be converted.
- If the array layout needs to be edited, use the Edit Layout,
Assign GIPO
fields, and
Assign Quant
fields wizards
- Select the project output folder (i.e. directory) to place the converted
data
- (Optionally) save the edited Array Layout in case you want to use
it again in the future.
- Press "Run" to convert the data.
- Press "Done" when the conversion is finished.
- Go to the project directory and then to the MAE sub-directory
(listed after step 4).
Click on the "Start.mae" file to start MAExplorer on the next
data. This assumes that you have previously installed MAExplorer.
|
The details on Cvt2Mae including more description, PDF examples of conversions
for several different types of arrays, the download area, status of the converter,
etc. are available on the Cvt2Mae home page
MAExplorer requires the data in the GIPO and Quant files be specified
by a spot position. This is indicated by the array spot geometry of
(#fields, #grids, #rows/grid, #columns/grid). The #fields is the
number of duplicated sets of grids if available - it is 1
otherwise. This 4-tuple must be specified in the Configuration file.
However, some array data does not have a spot geometry position data
available. The alternative is to generate a pseudoarray geometry. This
is possible since the pseudoarray image in MAExplorer is used simply
to indicate success of the data filter or relative differences
depending on the "Plot | Show Microarray" option. In Cvt2Mae we
generate a visually appealing pseudoarray image geometry if no array
geometry is specified with the data (e.g. Affymetrix data, etc). The
algorithm presented below will generate a geometry
(nGrids,nGridRows,nGridCols) that is compatible with the
visual use of the pseudoarray. The only assumption is the
nRowsExpected, the number of spots in the microarray (rows in
the database input file). The number of spots in the array is computed
automatically and the option to use the pseudoarray instead of the
actual array geometry is selected in the
Edit Layout Wizard for Grid Geometry.
OPT_GRID_SIZE = 1200; /* Optimal grid size for MAExplorer viewing */
ROWS_TO_COLS_ASPECT_RATIO = 3.0/4.0; /* desired rows/cols aspect aspect for a grid */
extra = 0; /* # of extra grid cols required */
/* Estimate # of grids. Assume a square aspect ratio */
if(n <= OPT_GRID_SIZE)
nGrids = 1;
else
nGrids = (n / OPT_GRID_SIZE)+1;
/* Estimate rows (r) and columns (c) from a rectangular grid
* where cols = (4/3) rows.
* Then, c = (4/3)r and r*c= area.
* Then (4/3)*r*r = area or
* r = sqrt((3/4)*area).
*/
if(nRowsExpected > 0)
while(true)
{ /* iterate to optimal size */
gridSize = n/nGrids;
nGridRows = sqrt( ROWS_TO_COLS_ASPECT_RATIO * gridSize );
nGridCols = (nGridRows / ROWS_TO_COLS_ASPECT_RATIO);
nGridCols += extra;
estTotSize = (nGrids * nGridRows * nGridCols);
if(estTotSize > nRowsExpected)
break;
else
extra++; /* keep trying until meet criteria */
} /* iterate to optimal size */
