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Table 5 Comparisons of the results obtained in Second 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 & DESeq2 RSEM & DESeq2 Centroid & DESeq2 Unique & edgeR RSEM & edgeR Centroid & edgeR
TopHat(unique) & cuffdiff 56 36 2 2 2    
TopHat(rescue) & cuffdiff 36 36 1 1 1    
Unique & DESeq2 2 1 9 7 5    
RSEM & DESeq2 2 1 7 19 6   3  
Centroid & DESeq2 2 1 5 6 12 1   1
Unique & edgeR      1 1   1
RSEM & edgeR     3    4  
Centroid & edgeR      1 1   1
  1. Even in this case, the comparison of DE analyses show a significant disagreement on the selection of DE genes. The values on the diagonal (in bold) are the results obtained from each method