I have a dataset with 159 tumors and 113 normal samples. I did differential analysis using
edgeR and selected differential expressed genes based on Foldchange > 2 and FDR < 0.05 (Tumors vs Normal). From differentially expressed genes I selected upregulated genes based on positive logFC. Among the upregulated genes I could see a gene
FAP which I'm interested in.
FAP is upregulated gene in Tumors when compared to Normal samples.
But when I plotted the expression (logCPM) of gene
FAP between Tumors and Normal samples I see that p-value is significant but shows that expression is higher in Normal samples. Here is the box plot.
Why this gene is upregulated in Tumors with
edgeR and in the box plot it shows higher expression in Normals? Why so different in different analysis? Anything wrong?
P.S. I calculated logCPM after filtering out low expressed genes