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Table 4 Examples of results of the First Trial

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

GENE: OTTHUMG00000031027|HLA-DRB5
FUZZY COUNTS Control Case Under-expr. Same-expr. Over-expr.
Tr[18,24,26,428] Tr[3732,4551,4666,6386] 1 0.003 0
ESTIMATED COUNTS Control Case STATS p-value Log2(FC)
 TopHat-unique (RPKM) 0.2 250.7 cuffdiff 0.9996 10.3
 TopHat-rescue (RPKM) 0.2 219.5 cuffdiff 0.9985 10.5
 Uniquely mapping 18 3732 FDR 0 7.6
 RSEM 23 4665 FDR 0 7.6
 Centroid 25 4607 FDR 0 8.1
GENE: OTTHUMG00000036468|TTTY15
FUZZY COUNTS Control Case Under-expr. Same-expr. Over-expr.
Tr[0,1,1,17] Tr[43,43,43,52] 0.024 0.986 0.007
ESTIMATED COUNTS Control Case STATS p-value Log2(FC)
 TopHat-unique (RPKM) 0 0.4 cuffdiff 0.0218 Inf
 TopHat-rescue (RPKM) 0 0.4 cuffdiff 0.029 Inf
 Uniquely mapping 0 43 FDR 1E-14 5.5
 RSEM 1 43 FDR 2E-14 4.5
 Centroid 1 43 FDR 2E-14 4.9
GENE: OTTHUMG00000129909|IGJ
FUZZY COUNTS Control Case Under-expr. Same-expr. Over-expr.
Tr[0,0,291,318] Tr[0,0,1227,1246] 1 1 0.217
ESTIMATED COUNTS Control Case STATS p-value Log2(FC)
 TopHat-unique (RPKM) 16.4 84.9 cuffdiff 0.0218 2.4
 TopHat-rescue (RPKM) 17.9 88.4 cuffdiff 0.029 2.3
 Uniquely mapping 0 0 FDR 1 0.0
 RSEM 250 1165 FDR 2E-208 2.2
 Centroid 146 614 FDR 9E-103 2.7
  1. The first gene, HLA-DRB5, despite the abundant presence of multireads in its read counts, shows a certain result, with an maximum under-expression possibility and very low same-expression possibility. This results is not confirmed by cuffdiff, evenif it computes a high FC. The second gene, TTTY15 result is not reliable because it has low read counts, but it is considered as a DE result by all the tools. Our method higlights the result as false positive, with a high same-expression value, because of the low mean expression values obtained. The third example, the IGJ gene, is a possible false positive. Its counts are quite low and its fuzzy read counts are mostly overlapping. The pvalues obtained by the other tools are confirmed by a high under-expression possibility, but the risk of having a false positive is pointed out by a high same-expression possibility
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