Hi everyone!

I am doing a deferentially expressed analysis with DESeq2, but now i have a doubt about using the contrast.

I have my info table of all samples that for example condition A, I have x, y,w,z different variables but I am only interested in analyse the deferentially expressed genes in y vs z, and what I do was using all samples and all condition, but I define the contrast=c("A","y",z") , but when i subset the info table and counts table for only samples and condition that i am interested and again i use the same contrast but this time the only variables is y and z, the results are different, that is in one analysis i have more genes than the other analysis. Someone can tell why this may happen and what I have to use, because I do not understand the differences.

Thanks for your help!

Thanks for your reply! But I thought that aren't important use the samples that are not in my contrast and because I am doing a PCA and heatmap and I only can show in these graphs the samples of these two variables. So you thing that for a set of samples I should use always the complete matrix of counts but defining the contrast with only the variables that I want??

Thanks a lot!

Provided all the rest of your samples are of good quality.