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 |