Index

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adjusting
all threshold slider values, 2.3.4
Applets
definition of Glossary
problems with 4.
suggestions 4.2
arrays
definition, 1.
using MAExplorer with your, C.
background,
correction 2.4.2.1
Beta,
level of software Overview
revision history 4.2
browsers,
problems 4.
suggestions 4.2
bugs,
list of known 4.
calibration, (see normalization),
[CB], menu item is a checkbox 2.
clones
referred to as gene in MAExplorer overview
closing
MAExplorer 1.5
popup windows 1.3
clustering,
genes, tutorial B.
cluster counts, plots 2.4.5.2
clustergram 2.4.5.4
definition 3.2.2
   similar genes 3.2.2.1
   similar genes 3.2.2.2
   similar genes 3.2.2.3
dendrogram 2.4.5.4
hierarchical, plots 2.4.5.4
K-means clustering, plots 2.4.5.3
similar genes, plots 2.4.5.2
clustergram 2.4.5.4
hierarchical clustering 2.4.5.4
K-means clustering 2.4.5.3
collaborator database 2.1
command history,
logging 2.5.2
popup window 2.5.2
condition
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 2.4.4.1
setting threshold 3.4
Cy3/Cy5
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 2.4.4.1
dendrogram,
hierarchical clustering 2.4.5.4
design of MAExplorer
design issues E.
design philosophy 3.1.2
evolution from 2D gel systems 3.1.3
Flicker 3.1.3
GELLAB-II 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)
displaying,
cluster plots 2.4.5
expression profiles 2.4.4.4
histograms 2.4.4.3
microarray image 1.3, 2.4.4.1
scatter plots 2.4.4.2
downloading MAExplorer,
installing on your computer D.2
updating, MAExplorer.jar Install 1.3
duplicate
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
editing,
menu 2.3
set from current cluster 2.4.5.3
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
displaying 2.4.4.4
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
reports 2.4.6.3.1
scatter plots 2.4.4.1
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 2.4.3.1
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
GELLAB-II
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
GeneClass,
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 2.4.6.2
saving gene sets as disk files 2.3.2
user defined 2.3.1, 2.4.4.1
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
groupware,
definition 2.1.1
menu 2.1
sharing user states 2.1
guesser,
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 2.4.5.4
ClusterGram plot 2.4.5.4
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
image,
displaying microarray 1.3, 2.4.4.1
intensity
background correction 2.4.2.1
expression thresholding 2.4.3
normalization 2.4.2.2
quantification 1.2
spot intensity thresholding 2.4.3
threshold Filter 2.4.3
introduction 1.
K-means,
description 2.4.5.3,
current cluster 2.4.5.3
edited gene list 2.4.5.3
mAdb
NCI/CIT MicroArray DataBase server F.
accessing through MAExplorer 2.4.4
merging data for multiple projects 4.1.9
MAExplorer,
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
menus,
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
meta-grid
handling in MAExplorer 1.1
handling non-standard in Cvt2Mae C.6
microarray,
description 1.1,
normalization 2.4.2.2
quantification 1.2, 3.3
mouse-over info 2.5
negative data,
Filter, positive data 2.4.3
normalization,
background correction 2.4.2.1
between microarrays 2.4.2.2
by 'Calibration DNA' 2.4.2.2
by HP mean & variance, Zscore 2.4.2.2
by HP mean & variance logs, Zscore 2.4.2.2
by HP mean & abs. variation logs, Zscore 2.4.2.2
by HP median 2.4.2.2
by HP log median 2.4.2.2
by scaling to 65K 2.4.2.2
by 'User Gene Set' 2.4.2.2
menu 2.4.2
views, improving 2.4.2.3
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
plots,
cluster 2.4.5
displaying microarray 1.3 (see displaying)
exploratory 3.
expression profile 2.4.4.4
histograms 2.4.4.3
menu 2.4.4
scatter plots 2.4.4.2
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
pseudoarray
Cvt2Mae, algorithm Cvt2Mae Desription
display of 2.4.4.1
geometry definition 1.1
image, changing type 2.4.4.1
types of displays 1.3
pseudoimage
p-value
Filters, using 2.4.3
pseudoarray display of 2.4.4.1
[RB], menu item is a radio button 2.
ratio
definition 2.4.3
histogram 2.4.4.3
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 2.4.6.3
Excel format 2.4.6.3
fonts 2.4.6.4
formats 2.4.6.3
genes 2.4.6.2
mouse-over info 2.5
samples 2.4.6.1
/Report directory C.
/State directory C.
RLO (R LayOut) analyses,
RLO methods 2.6
Update RLO methods 2.1
Update RtestPlugin 2.1
Updating,
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
quantification,
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
scrollers,
multiple scrollers 2.4.3.1
setting parameters 2.3.4
sets,
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
statistics,
setting thresholds 2.3.4
reports of 2.5.4
use in gene Filter 2.4.3
table format 2.4.6.3
thresholding,
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
updating,
MAExplorer program Install 1.3, 2.1
MAEPlugins jar files 2.1
user gene list,
editing 2.3.1
showing 2.4.4.1
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 2.4.2.3
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