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all threshold slider values, 2.3.4
definition of Glossary
problems with 4.
suggestions 4.2
definition, 1.
using MAExplorer with your, C.
level of software Overview
revision history 4.2
problems 4.
suggestions 4.2
list of known 4.
calibration, (see normalization),
[CB], menu item is a checkbox 2.
referred to as gene in MAExplorer overview
MAExplorer 1.5
popup windows 1.3
genes, tutorial B.
cluster counts, plots
definition 3.2.2
   similar genes
   similar genes
   similar genes
hierarchical, plots
K-means clustering, plots
similar genes, plots
hierarchical clustering
K-means clustering
collaborator database 2.1
command history,
logging 2.5.2
popup window 2.5.2
current condition 1.1,
definition 1.1, 2.2
F-test on current OCL 2.4.3
named sets, editing 2.2.6
Ordered Condition Lists (OCL), editing 2.2.7
using Edit menu 2.3, 2.3.3
configuring MAExplorer,
for other arrays C.
Conversion of microarray data files,
converting to MAExplorer format E.
Cvt2Mae C.
home page Cvt2Mae
current gene,
click on gene in image or 2Dplot 2.4.4
click on Clone_ID in Report 3.2
data mining, used in 3.3
definition 1.1
setting 1.1
current cluster,
current cluster 2.4.5
edited gene list 2.4.5
current HP sample 1.3
custom databases,
creating 1.5
CV filtering,
F1 F2 2.4.3
X & Y sets 2.4.3
E list 2.4.3
pseudoarray display of
setting threshold 3.4
accessing Cy3/Cy5 data as F1/F2 1.1
data, Cy3 vs Cy5 for current HP 3.4
data, HP-X (Cy3 or Cy5) vs HP-Y (Cy3 or Cy5) 3.4
Filter by Cy3/Cy5 data 1.1
flipping Cy3 Cy5 data per sample 1.1, 2.2.2
intensity, for Cy3/Cy5 data 1.1
pseudoarray display for Cy3/Cy5 data 1.3
ratio calculation 2.4.2
ratio median correction 2.4.2
reports for Cy3/Cy5 data 2.4.6
scatter plots for Cy3/Cy5 data
hierarchical clustering
design of MAExplorer
design issues E.
design philosophy 3.1.2
evolution from 2D gel systems 3.1.3
Flicker 3.1.3
WebGel 3.1.3
2DWG database 3.1.3
DetValue spot data,
Filter, by Spot Detection Value 2.4.3
DetValue definition C.3.1
directories, used by MAExplorer (see folders)
cluster plots 2.4.5
expression profiles
microarray image 1.3,
scatter plots
downloading MAExplorer,
installing on your computer D.2
updating, MAExplorer.jar Install 1.3
genes Glossary
spots 1.
dye-swap experiments 2.2.2
experimental design 3.1.1
Dryrot fatal errors
definition 4.4
handling 4.4
Edited Gene List (EGL)
definition 2.3.1
manipulating 2.3.1, 2.3.2
Filter, use in 2.4.3
showing in pseudoarray 2.3.1, 2.5
menu 2.3
set from current cluster
setting genes subset 1.1
user 'edited gene list' 2.3.1
examples, demo
applets A.
creating MAExplorer files for your data C.
stand-alone A.
exploratory analysis
methods of 3.
overview 1.4
plots 1.4
SaveAs DB - saving the state 1.4.1
user state 2.1
exiting MAExplorer 1.5
expression profiles,
clustering, part of tutorial B.
definition 3.2.1
HP-E 'list of samples Overview
plot, tutorial B.
F1F2 - replicate spots per gene,
accessing Cy3Cy5 data as F1F2 1.1
definition 1.1
CV spot filtering 2.4.3
scatter plots
figures list of, Figs
Filter, gene data
by Cy3/Cy5 ratio 2.4.3
by good spots data 2.4.3
by positive data 2.4.3
by sample intensity 2.4.3
by sample ratio 2.4.3
by spot CV 2.4.3, 2.4.3
by spot intensity 2.4.3
by threshold 2.4.3
by user defined gene list 2.3.1
Filter menu 2.4.3
tutorial B.
using multiple scrollers
Venn diagram, 1.3
flipping Cy3 and Cy5 channels
swapping per-sample 2.2.2
folders, used by MAExplorer
list of all folders C.
/Cache C.
/Config C.
/MAE ( C., D.4)
/Images C.
/Plugins C.
/Quant C.
/Report C.
/Plugins C.
fonts, text
changing 2.3.4
basis for MAExplorer paradigm 3.1.1
for data mining 3.1.1
groupware 2.1.3
GenBank, access from
gene in image 2.5
gene in scatter plot 2.5
gene report 2.4.6
Automatic naming based on Gene NameC.4
menu 2.4.1
subsets 2.4.1
gene lists,
gene Filter menu 2.3
gene sets menu 2.3.2
reports of
saving gene sets as disk files 2.3.2
user defined 2.3.1,
gene-gene table C.4
gene name,
current gene, setting 1.1
displaying 3.3
Gene Class naming based onC.4
good spot data,
Filter, Good Spot data 2.4.3
Grid,Row,Column encoding
alternative encoding: NAME_GRCC.4
definition C.4
handling non-standard C.6
meta-grid 1.1
definition 2.1.1
menu 2.1
sharing user states 2.1
for setting current gene 1.1
for setting current gene 2.3.1
setting E.G.L. subset 2.3.1
wild card gene names 2.3.1
Help menu 2.6
hierarchical clustering
ClusterGram plot
hybridized sample (HP),
current 1.3
HP-E 'list of samples Overview
Samples menu 2.2
selecting a particular HP 2.2.1
sets of HP-X and HP-Y 1.3
sets of HP menu 2.3.3
displaying microarray 1.3,
background correction
expression thresholding 2.4.3
quantification 1.2
spot intensity thresholding 2.4.3
threshold Filter 2.4.3
introduction 1.
current cluster
edited gene list
NCI/CIT MicroArray DataBase server F.
accessing through MAExplorer 2.4.4
merging data for multiple projects 4.1.9
command history window 2.5.2
exiting 1.5
menu summary 2.
messages logging window 2.5.1
overview Overview
starting 1.5
Master gene ID,
definition 1.1
detailed descriptions 2.
  1. Cluster 2.4.5
  2. Edit 2.3
  3. File 2.1
  4. Filter 2.4.3
  5. GeneClass 2.4.1
  6. Help 2.7
  7. Normalization 2.4.2
  8. Plot 2.4.4
  9. Plugins 2.6
  10. Report 2.4.6
  11. Samples 2.2
  12. View 2.5
summary 2.
RLO methods 2.6
messages from MAExplorer,
logging 2.5.1
popup window 2.5.1
handling in MAExplorer 1.1
handling non-standard in Cvt2Mae C.6
description 1.1,
quantification 1.2, 3.3
mouse-over info 2.5
negative data,
Filter, positive data 2.4.3
background correction
between microarrays
by 'Calibration DNA'
by HP mean & variance, Zscore
by HP mean & variance logs, Zscore
by HP mean & abs. variation logs, Zscore
by HP median
by HP log median
by scaling to 65K
by 'User Gene Set'
menu 2.4.2
views, improving
Open disk DB 2.1
ontologies of gene names
Gene Class subsets 2.4.1
simulating with Gene Sets 2.4.1
Ordered Conditions List (OCL)
current OCL 1.1,
definition 1.1, 2.2
F-test on current OCL 2.4.3
conditions, editing 2.2.6
discussion 2.2.7
overview Overview
cluster 2.4.5
displaying microarray 1.3 (see displaying)
exploratory 3.
expression profile
menu 2.4.4
scatter plots
tutorial B.
popup windows
closing 1.3
definition 1.3
preferences 2.3.4
presentation mode 2.5
projects 2.1
login required 2.1
public/collaborator 2.1
switching between 2.1
Cvt2Mae, algorithm Cvt2Mae Desription
display of
geometry definition 1.1
image, changing type
types of displays 1.3
Filters, using 2.4.3
pseudoarray display of
[RB], menu item is a radio button 2.
definition 2.4.3
reports of gene 2.4.6
threshold Filter 2.4.3
Zscore, used instead of ratio 1.2
recommended hardware Overview
references 4.2
replicate genes Glossary
reports 2.4.6
dynamic format
Excel format
mouse-over info 2.5
/Report directory C.
/State directory C.
RLO (R LayOut) analyses,
RLO methods 2.6
Update RLO methods 2.1
Update RtestPlugin 2.1
MAExplorer program 2.1
MAEPlugins 2.1
RLO methods 2.1
QualCheck spot data,
Filter, by Spot Quality 2.4.3
QualCheck codes C.4.1
QualCheck definition C.3.1
of microarrays 1.2
reporting 3.3, 3.3
saving gene sets as disk files 2.3.2
saving plots and text reports
saving plots 1.1
saving text windows 1.1
multiple scrollers
setting parameters 2.3.4
gene sets menu 2.3.2
gene subsets 3.4
HP sets menu 2.3.3
of HP-X and HP-Y 1.3
of HP-E Overview
stand-alone version,
application, use of D.
downloading D.2
format, .mae file D.3
installing D.1
saving gene sets as disk files 2.3.2
starting with .mae files D.1
updating, MAExplorer.jar Install 1.3
starting MAExplorer,
custom Applet DB 1.5
quick start 1.5
stand-alone DB 1.5, D
with particular sample 1.5
setting thresholds 2.3.4
reports of 2.5.4
use in gene Filter 2.4.3
table format
set by scrollbars 3.6
set by histogram bin 3.2
use in Filter 2.4.3
tutorial 1.5
advanced Appendix B
short introductory Appendix A
MAExplorer program Install 1.3, 2.1
MAEPlugins jar files 2.1
user gene list,
editing 2.3.1
user state,
definition 2.1.1
groupware access to 2.1
menu 2.1
views, of the data 2.5
active Web mode 2.5
color scheme mode 2.5
gang F1-F2 scrolling 2.5
mouse-over info 2.5
normalization, improving
presentation mode 2.5
view E.G.L.. mode 2.5
Web databases,
accessing dbEST 2.5
accessing GenBank 2.5
accessing GeneCard 2.4.6
accessing mAdb Gene Report 2.5
accessing MGAP histology 2.4.6
accessing MGAP models 2.4.6
accessing UniGene 2.5
wild card names in guesser,
setting genes subset 1.1
specifying names 1.1