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Table 8 Comparison of the number of groups detected in the C2.KEGG category and of the number of common detections in three datasets

From: Functional Analysis: Evaluation of Response Intensities - Tailoring ANOVA for Lists of Expression Subsets

0.010 A2.
fixed
Faeri.
fixed.null
Faeri.
fixed.perms
GSA.
mean*
GSA.
absmean*
GSA.
maxmean*
Globaltest.
asymptotic
Globaltest.
gamma
Globaltest.
permutations
Gsea.
pval
Gsea.
fdr
Samgs.
pval
Samgs.
qval
Emexp445 62 7 14 14 5 19 0 8 0 0 0 0 0
GSE-1056 36 9 51 5 0 8 1 15 0 0 0 0 0
GSE-4086 93 89 94 49 38 62 0 0 0 0 0 NA NA
Emexp445-GSE-1056 5 0 6 1 0 0 0 1 0 0 0 0 0
Emexp445-GSE-4086 24 5 9 8 0 11 0 0 0 0 0 NA NA
GSE-1056-GSE-4086 21 7 37 4 0 4 0 0 0 0 0 NA NA
Emexp445-GSE-1056-GSE-4086 4 0 3 1 0 0 0 0 0 0 0 NA NA
0.050 A2.
fixed
Faeri.
fixed.null
Faeri.
fixed.perms
GSA.
mean*
GSA.
absmean*
GSA.
maxmean*
Globaltest.
asymptotic
Globaltest.
gamma
Globaltest.
permutations
Gsea.
pval
Gsea.
fdr
Samgs.
pval
Samgs.
qval
Emexp445 62 18 42 14 5 23 26 45 0 0 0 0 0
GSE-1056 51 27 80 8 2 12 33 70 40 11 0 15 69
GSE-4086 119 119 142 49 38 62 32 185 0 0 0 NA NA
Emexp445-GSE-1056 15 6 34 1 0 0 4 20 0 0 0 0 0
Emexp445-GSE-4086 48 14 37 8 0 13 13 44 0 0 0 NA NA
GSE-1056-GSE-4086 31 23 71 4 1 6 7 69 0 0 0 NA NA
Emexp445-GSE-1056-GSE-4086 13 4 31 1 0 0 2 20 0 0 0 NA NA
  1. The results are shown for each method, for significance thresholds of 0.05 and 0.01. The three datasets analyzed are E-MEXP-445, GSE-1056 and GSE-4086, and concern the same condition (oxygen deprivation). The first column contains the datasets analyzed. The first 3 rows of each table contain the top list obtained by each geneset analysis method. When several datasets are mentioned at the beginning of the row, the number of genesets in the other columns is the intersection of the results from different datasets