I have RNA-seq data with 2 conditions and 3 replicates per conditions.
I analysed differentially expressed genes with
With a treshold of 1 log2FoldChange and 0.01 padj in
DESeq2: 14400 /32000 (45%) of DE genes
With a treshold of 0.01 pval in
Ballgown: 3678/32000 (of DE genes), even with no fold change treshold, the number of DE genes is (very) lower. In ballgown, what is the difference between qval and pval ? Which one corresponds to padj in DESeq2 ?
I expect many DE genes as conditions are very different biogically (testis vs ovary, same species).
Why do I have a so large difference between softwares?