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?
Answered by the DESeq2 author: https://support.bioconductor.org/p/131401/
If you use too small a subset, the assumptions underlying the normalization procedure may be violated.
One assumption is, that the majority of genes are not differentially expressed.
Login before adding your answer.
Use of this site constitutes acceptance of our User Agreement and Privacy