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Table 2 Number of DE genes from sex chromosomes detected by three method in the HapMap-CEU data set at a FDR-adjusted p-value of 0.05

From: aFold – using polynomial uncertainty modelling for differential gene expression estimation from RNA sequencing data

Method Sex1/Total2 Sex in Top 10 (Rank)
p-value Fold-change
aFold 7/8 7 7
DESeq2 7/12 7 5
Voom 7/7 7 5
edgeR 7/20 7 5
ABSSeq 7/7 7 7
baySeq 7/15 7 5
ROTS-t 7/8 7 5
ROTS-q 7/8 7 5
  1. Number of genes identified by each methods in sex chromosomes (1) and total (2)