I'm working with RNA-seq data. I have 40 tumor samples and 5 Normal samples. Differential analysis with
Deseq2 based on Fold change > 1.2 and alpha < 0.05 gave very low number of differentially expressed genes. Only 2 upregulated genes.
res <- results(dds, lfcThreshold = log2(1.2), alpha = 0.05)
To get more number of differential expressed genes I have few questions now
1) Instead of FDR < 0.05 can I use FDR < 0.1 (or) FDR < 0.5. Will there be any low confidence with this?
2) Can I select differential expressed genes only based on FDR < 0.05 without any fold change cutoff?
3) As I get very low number of DEGs with FDR < 0.05 & Foldchange > 1.2, Can I select DEGs based on Foldchange > 1.2 and p.value < 0.01 or 0.05 ?
PCA of the samples looks like this