Hi, I do the DESeq2 analysis of RNA-seq samples from two different tissues, each with 3 replicates, and both PCA or sample correlation heatmap results is normal and as expected. The total diffrential gene number has reached ~60% (padj<0.1), this did not obey the DESeq2 assumption that most of genes are not diffrentially expressed. So using DESeq2 may not be appropriate.
I search for two related posts: https://support.bioconductor.org/p/94661/ & Differential expression for two very different samples. But I still cannot find the good solution for the case.
I know there must be a large proportion of genes differentially expressed between the tissues, the problem is how to identify them in a correct way? I think many of you may encounter this phenomenon when analysis RNA-seq samples between different tissues. How do you figure out this?
Thank you very much!