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

BMC Bioinformatics

Table 3 Comparison of the results obtained in First Trial

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

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

ISSN: 1471-2105