I have RNA-Seq data for LUNG cancer. 370 tumor and 50 Normal. For differential analysis initially I did some filtering and kept approx. 19k genes for further analysis. I used edgeR.
With a FC > or < 2 and FDR < 0.05
tr <- glmTreat(fit, contrast=contrast.matrix, lfc = log2(2))
I got approx 3000 differentially expressed genes.
Among the 3000 differentially expressed genes I'm interested in a gene
GeneSymbol logFC unshrunk.logFC logCPM PValue FDR OIT3 2.156487448 2.171599487 -0.437234244 0.000701037 0.005304312
I see the above gene
OIT3 is Upregulated. Why I see logCPM with negative value?
And I plotted the logCPM expression of the above gene and did a t-test which gave pvalue 0.1 which means not significant.
1) I see the gene is differentially expressed with Differential analysis using edgeR. Why I see logCPM with negative value?
2) With t-test why it is not significant?