Differential gene expression DGE by colored scatter plot
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6.9 years ago

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
R • 2.3k views
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Why don't you just use GFOLD instead of trying to come up with your own method?

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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?

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You'd be better off to borrow someone's mac laptop than to do what you're trying on Windows.

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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.

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