Dear all,
I have list of differentially expressed miRNAs (DESeq2 output) and want to choose about 10 important candidates for downstream analysis (GO analysis with targets of selected miRNAs).
I was wondering what could be a good balance in selecting these miRNAs considering both baseMean and the Log2FoldChange?
Is it a good idea to first rank the differentially expressed miRNAs based on the Log2FoldChange and then select the 10 candidates based on having highest baseMean?
What could be your suggestions?
Thank you
Thank you @Trivas for your answer - The thing is that, with baseMean over 100 because I feel that they have most likely regulatory impact. This is of course slightly a philosophical topic but imagine if a DE miRNA has a big l2FC and very low padj, but then baseMean is around 20, would you consider this candidate to have a robust effect in a cell by itself? Or insted the same situation but with a baseMean over 100?