I am using DEseq2 to quantify the gene expression of a very limited set of non coding genes.
It might be obvious, but can I still trust the significance of the differential expression that I obtain, or would having a limited set of genes cause some genes that are not strongly differentially expressed to appear as significantly differentially expressed?
How does selecting a part of the genes only impact the final assessment of the differential expression - so if I was running the same differential expression with these genes along with a full annotation set such as all the ensembl genes, would I still find the same genes as significantly differentially expressed? (without thinking of the obvious change due to the quantification of the raw reads itself which would undoubtedly be slightly different due to gene overlap)
Many thanks, Delphine