edgeR calculate CPM instead of lof2FC

Olha · 02-10-2016, 03:09 PM

Dear, SEQanswer community,

I want to detect differentially expressed genes between tumor and normal
tissue, adjusting for any differences between the patients.
I have 8 leukemia patients and 8 healthy donors.
I follow the edgeR manual, particularly case study at chapter 4.1.

I use the following commands:

Code:

> fit <- glmFit(counts, design)
> lrt <- glmLRT(fit)
> topTags(lrt)
> colnames(design)
> o <- order(lrt$table$PValue)
> cpm(counts)[o[1:10],]

This provides me top 10 CPM values for each of my sample. However, my goal is to get the log2FC for each sample.

In what way I can calculate log2FC for each sample instead of CPM values in edgeR?

Thank You very much for help!

Olha

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02-10-2016, 03:09 PM	#1
Olha Junior Member Location: Columbia, MO Join Date: Sep 2015 Posts: 6	edgeR calculate CPM instead of lof2FC Dear, SEQanswer community, I want to detect differentially expressed genes between tumor and normal tissue, adjusting for any differences between the patients. I have 8 leukemia patients and 8 healthy donors. I follow the edgeR manual, particularly case study at chapter 4.1. I use the following commands: Code: > fit <- glmFit(counts, design) > lrt <- glmLRT(fit) > topTags(lrt) > colnames(design) > o <- order(lrt$table$PValue) > cpm(counts)[o[1:10],] This provides me top 10 CPM values for each of my sample. However, my goal is to get the log2FC for each sample. In what way I can calculate log2FC for each sample instead of CPM values in edgeR? Thank You very much for help! Olha Last edited by Olha; 02-10-2016 at 03:10 PM. Reason: incorrect title