Im really stuck with this one so any help would be appreciated.
I have the expression data for 28 different tissues. The matrix I create will look something like below but with 28 tissues and around 50k rows:
tissue1 tissue2 tissue3 .....etc.... gene1 gene2 gene3 etc..
I'm going to use limma's "normalizeBetweenArrays()" function to quantile normalise the data. I cant figure out whether I should be filling the matrix with the raw rpkm values or the log2 normalised values for entry into the limma function. Which one should it be?
EDIT: I do get how quantile normalisation works, but I just dont know whether it is correct to use it on log2 values. I have read some resources on this hwoever no one is clear about what the input is.