I run DESeq2 program on 52 tumor Vs only 3 normal samples.
Applying >=0.05 cutoff on adjusted p values and |logFC>=1| was resulted to 1450 up-regulated Vs 440 down-regulated genes.
Now my question is:" is this large numbers of de-regulated genes has been caused by the very small number of normal samples?"
How can I tackle the problem of the small size of normal samples? Is it reasonable to apply more stringent cutoff on logFC or adjusted p-values?
Is it acceptable if I work on these large number of deregulated genes and report them?
I am looking forward to your comments