I have 30 tumor and 3 normal samples. MDS plot looks like this Tumor vs Normal I have used edgeR and selected differential expressed genes based on Fold change greater than 1.2 and FDR < 0.05. Differential analysis between tumor and normal gave only two upregulated genes.
So, I thinking to apply random selection of samples. Selecting random samples from tumor condition and do differential analysis with that and repeat the process
n times. This gives different set of genes differentially expressed in different analysis.
But not sure how to select final differentially expressed genes because same gene can be differentially expressed in different analysis with different fold change and fdr values.
1) Do you think applying subsampling for this a right choice? If not when subsampling can be applied?
2) As I get only 2 upregulated genes with FC > 1.2 and FDR < 0.05, can I increase the FDR to 0.5 or 0.1 to get more upregulated genes? Is selecting genes based on FDR < 0.5 or 0.1 a right choice?