I have 5 rna seq samples for one group and 10 samples in another group. For this organism there is no reference transcriptome. I have assembled them using trinity and did assembly again by combining all samples to get master transcriptome. I have around 200k unique transcripts. I used RSEM to calculate abundance estimation and edgeR to get differential expression and normalized transcripts. Now i have 15 columns with the normalized fpkm values. If i wanted to get the differential expression between two groups, how can i use this information ? what analysis i should perform to obtain this
If i understand you correctly; you have already done DE using edgeR then why you need to do it again?
If not: Use DEB service (edger; deseq bayseq,) for DE analysis: http://www.ijbcb.org/DEB/php/onlinetool.php