Entering edit mode
8.4 years ago
meettoo2000
•
0
I would like to visualize my NGS data using differential gene expression (DGE) using R However, I do have only one replica? I know its not good but that's a first trail. So I want to get the DGE and to highlight the highest expressed contigs in red color, with labeled name to identify these contigs. X= normal and Y= infected I have 213951 contigs in the both conditions my data set as follow. I need the command line to set up such data set (I am beginner in that filed)
Contigs ID Infected Normal
TR1|c0 56 43
TR213951IC1 79 1.4
Why don't you just use GFOLD instead of trying to come up with your own method?
Dear Devon Ryan many thanks for your replay, I search for GFOLD but it need Linux platform, I use windows platform not Linux or mac so that's why R is convenient. (I am not bioinformatics, just starting to learn). Plus I also want to know regarding the 0 values in the FPKM, if I use log2(FPKM+0.1) to off the 0 value is it ok? but the problem will raise that the small expressed one will get high fold change by this way?
You'd be better off to borrow someone's mac laptop than to do what you're trying on Windows.
I should note that you can also use DESeq (not DESeq2), which may produce useful results (with the obvious caveat that unreplicated experiments never produce robust results). That's in R.