Differential gene expression analysis

Question

[ATCG]

I am performing differential gene expression using DESeq2 but will be subsetting transcripts based on a pre-determined criterion. Does this sub-setting violate any assumptions make by the statistical package?

[ATpoint]

Answered by the DESeq2 author: https://support.bioconductor.org/p/131401/

Answer 1

[swbarnes2]

If you use too small a subset, the assumptions underlying the normalization procedure may be violated.

[caggtaagtat]

One assumption is, that the majority of genes are not differentially expressed.