DESeq2 for specific genes

Question

[andreiareis1987]

Hi, I have a quick question/doubt what is the best approach to do. I have RNA-Seq data and i am doing the full workflow after getting the DEGs and iam trying to match them with a list of genes that are involved in specific pathways. I have a doubt if i can also after normalization filter the genes and get only that are in the list of specific pathways and perform de results() function or this approach is wrong? Thanks in advance, All the best. Andreia

Answer 1

[swbarnes2]

Don't do that. Just do the whole experiment properly with all the genes, then filter down to what you want to look at.