Dear all, please would you confirm the following :

shall we have as input in DEseq2 all the RNA-seq data that was generated in 4 different conditions (let's say):

<> C1
<> C2
<> C3
<> C4

when the baseMean X is computed, is it supposed to be the same, regardless of the contrasts that we make ?

shall we extract the contrast C1 vs C2 : the reported baseMean is supposed the same X as above ?

we extract the contrast C3 vs C4 : then the reported baseMean is still X, correct ?

thanks a lot !

~ Bogdan

More information about the columns is here:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-to-all-calculated-values

The base mean is the mean of normalized counts in the dds.