I want to perform DESEq2 vst and rlog variance stabilising transformations on gene counts from two different tissue types in two different mammalian species. I have two questions:
Is there a disadvantage to performing vst/rlog only on a subset of genes that are significantly different in my DESeq2 DE analysis? or should I be doing these transformations on the entire GeneCount matrices?
Does it matter if I perform these transformations using a matrix that has -
a. ALL genecounts from both tissue types in both species or
b. has counts for both tissue types in A species or
c. has genecounts from A tissue type in both species?
shall be grateful for any advice!
Thanks in advance, Adi