sungheep / nanostring Goto Github PK

Dear, may I have some questions about edgeR you applied to Nanostring?

First, the input for edgeR is raw counts. So, your "nano_count.csv" is the raw counts from NanoString rather than normalized counts from nSolver by negative, positive and housekeeping controls, right?

I am trying to find out which is better to apply to NanoString for edgeR or DESeq2. Do you have any comments for normalization for NanoString? Here is a paper of DESeq2 about normalization for NanoString https://academic.oup.com/bib/article/22/3/bbaa163/5891144 .

Second, in your code, you used below ones for normalization, could you tell me what does it for "y <- y[keep, , keep.lib.sizes=T]"? and what is the default method for "calcNormFactors"?

y <- y[keep, , keep.lib.sizes=T]

y <- calcNormFactors(y)

Last, could you share me what is it looks for your "Nanostring_all.csv"? I did't follow your first few lines of codes for "group".

Really appreciate if you can see my questions, thanks a lot!

Best,

Xiaofei