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Table 1 Comparison of functionalities among AMDA and other software that perform a full microarray data-analysis The functionalities provided by AMDA are reported in the first column, with comment or list of methods or DBs where necessary. The remaining columns show whether other software that perform a full microarray data-analysis provided the same features. A plus indicate that the software provides it and, when applicable, the same set of methods. A minus indicates that the functionality is not provided. Text is used to report in case the provided features are different. Finally, italic text is used to identify functionalities for which the provided methods are a sub-set of those available in AMDA.

From: AMDA: an R package for the automated microarray data analysis

AMDA GenePublisher12 ExpressionProfiler5 GEPAS4 Array Pipe6 Race7 Midaw8 Sykaceket al.9
widget interface + a web page for each tool a web page for each tool a web page for each tool a web page for each tool a web page for each tool -
analysis of CEL files (signal,rma,gcrma,mbei) mbei + + no Affymetrix + no Affymetrix no Affymetrix
quality controls - - + + + + -
non-linear array normalization (quantile, qspline) qspline quantile + + quantile - house keeping and spike RNA
array hierarchical clustering + + + - - + -
replicates' scatter plot all pairs - manually - - - -
support of many experimental designs (common ref, time-course, 2 common ref, 2 time-course) only common reference manually with limma two class or multi-class - only two class comparison only two class comparison only balanced reference design
method for DEG selection (plgem, sam, FC, limma) t-test with BH correction limma, t-test t-test, anova, clear test t-test and method specific for spotted array empirical bayes FC, t-test. sam mixed anova model
selection of many DEG methods - - - - - - -
DEG heat-map + + not linked to DEG selection - - not linked to DEG selection -
gene normalization + + + - - + -
DEG clustering + + not linked to DEG selection - - not linked to DEG selection -
silhouette-evaluation of clusters + - - - - - -
functional evaluation of clusters (GO, KEGG, user-families) - GO and signature algorithm not linked to clusters selection, no user-families - - - -
functional evaluation of DEG (GO, KEGG, user-families) GO, KEGG GO and signature algorithm not linked to DEG selection, no user-families only export of annotated gene lists GO - -
functional summary - - - - - - -
writing of annotated gene lists - - - - - - -
correspondence analysis (bi-plot of arrays and genes) PCA(only arrays) + - - - PCA(only arrays) -
dynamic PDF generation + - - - - - -
flexible work-flow - + + + - - -
automation + - - - - - -
other tools not available in AMDA, notes array classification, promoter analysis, prediction of orphan function support to not affy, chr.local and sequence analysis numerous independent tools - - discriminant analysis (PAM) imputation of missing values