Hi all experts,
I have used Trinity software for doing de novo transcriptome assembly. Then, I used bowtie and RSEM within Trinity package for read mapping and counting. Finally, I got the raw count and FPKM value. I used raw count for doing differential expression analysis by edgeR software, say, I compared A-B library. I found that among DEG genes reported by edgeR software, some few genes with positive log fold change, meaning that the higher expression in A library in relative to B, have the lower FPKM value in A as compared with its FPKM value in B library. For instance, please consider the below example
logFC logCPM LR PValue FDR FPKM (B) FPKM(A)
c50354_g2_i5 2.825768038 5.659882391 41.70680491 1.06039E-10 6.64373E-07 118.187 18.093
As you could see the FPKM value of c50354_g2_i5 transcript are in 18.093 and 118.187 in the library B and A, respectively. But during the comparison A-B library, the log fold change is positive. Could you please explain to me what happened for such genes?
Thank you in advance