Hi, I am using limma for differential gene analysis of RNA seq results. I have encountered the following issues: I cannot find any genes with significant padj values (less than 0.05). Although some genes have extremely high logFC values. (I use TPM values for difference analysis)
But when I use DESeq to perform differential analysis on the same sample (using counts), I can normally obtain a set of differentially expressed genes.
I want to know what is causing this situation. All help will be greatly appreciated!
I will attach the limma code I used below.