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:
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
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],]
In what way I can calculate log2FC for each sample instead of CPM values in edgeR?
Thank You very much for help!
Olha