getting gene expression values using edgeR

Question

[GuriGuri1565]

I have 4 sample groups including 10 samples in each group. so total samples are 40.

I have questions. first, I want to get gene expression values using edgeR so I'll compare total samples, total gene expression values. Can I just use cpm function? otherwise, Should I use another function or value like TPM value? second, whan I use calcNormFactors function, What is meaning of norm.factor ? and why do one sample have one norm.factor value?

Answer 1

[h.mon]

I want to get gene expression values using edgeR so I'll compare total samples, total gene expression values.

What do you mean by "compare"? Perform some clustering analysis? Or perform differential expression analysis? For the former, the edgeR Users Guide recommends cpm(y, prior.count=2, log=TRUE), for the later, use raw counts and read carefully the guide for instructions.

second, whan I use calcNormFactors function, What is meaning of norm.factor ?

library(edgeR)
?calcNormFactors

Or, again, read edgeR Users Guide.

[GuriGuri1565]

I solved my problem. Thank you!