Hi,

I have a question regarding DEXSeq results I am getting. I used DexSeq for count table that I prepared. This count table contains only two isoform for each gene. I also have 3 biological replicates for control and treatment. 

When I get the result table, I realized that, isoform 1 and isoform 2 has different p-values and different log2FC values. Since DEXSeq compares expression of isoform 1 with isoform 2, I thought p-val for two isoform case supposed to be same, and log2FC suppose to be exact opposite.  For example:

groupID     featureID    pvalue    log2FC

Prdm4         1              0.82         -0.19

Prdm4         2              0.77          0.03

Can anyone help me to understand why I am getting different p-val and log2FC for two isoform comparison?

Thanks!

Ays