I have a question: I am just interested in a subset (a part of genes) of my raw count matrix. I tried to run DESeq2 with the subset and the complete matrix respectively. However, the DE result based on the subset is very different compared with the corresponding genes in the output based on the whole count matrix. In the subset only result, 90% of genes are down-regulated. But in the whole matrix based result, only 50% of genes which are from the subset are down-regulated.
I want to know is that correct: do DE analysis based on the subset rather than a complete count matrix?
edit: 1. I also tried limma + voom. The result is similar to the DESeq2. The subset appears 90% down-regulated. But the corresponding genes in the complete count matrix only appears 50% down-regulated.