RNA Seq Analysis with multiple samples

[empyrean]

Hi..

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.

[pbluescript]

I'm a bit confused about what you want to do. Are you asking how to perform differential expression or what to do after you have a list of differentially expressed genes?

[empyrean]

i performed differential expression by giving 15 samples as input to edgeR and it gave me a file name Filename.normalized.FPKM and it has values ranging from 0 to 800,000 . I think its not a fold change. so, how can i get some meaningful data out of two groups or is there a way where i can do differential expression diffently between two groups?