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Table 3 Comparison of the results obtained in First Trial

From: A fuzzy method for RNA-Seq differential expression analysis in presence of multireads

Results filtered by adjusted p-value < 0.05 and abs(log2(FC)) > 0.5 TopHat (unique)& cuffdiff TohHat (rescue)& cuffdiff Unique & FDR RSEM & FDR Centroid & FDR
TopHat (unique) & cuffdiff 17 12 12 13 15
TohHat (rescue) & cuffdiff 12 13 11 12 12
Unique & FDR 12 11 7170 3224 1244
RSEM & FDR 13 12 3224 4897 1381
Centroid & FDR 15 12 1244 1381 2159
  1. Each cell represents the number of DE genes in common between two methods specified in the corresponding row and column. Despite the Fisher’s test with FDR extracts a very large list of DE genes, all the results do not agree on at least one gene. The values on the diagonal (in bold) are the results obtained from each method