DEseq/ EdgeR RNaseq calculation of fold change
I was wondering if it is reasonable to use DEseq/ edgeR packages to call differential expression p values and then calculate the fold change out side packages (manually) just transforming the counts to log values and calculating sample 1 -sample 2? I understand that there is inbuilt option getting fold change with in these packages, but I would like to do it outside and have better manual control of data and rank genes via p and FC.
Thanks
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why don't you do everything outside like calculating p-values as well, so that you have much more control.
p value will be from Deseq just Fc will be outside the package and then I want to further rank genes between p and FC
Maybe you should make FC with limma, just to keep it simple ;-P