I have an expression matrix, its rows belong to different genes and columns belong to samples.
I want to do quantile normalization. But for me seems two ways to normalize it. First: row wise; normalize the expression of every gene in all samples. Second: normalize columnwise: normalized expression of all genes in one sample and then go to other sample and ....
Which one makes more sense?
Good point Devon. I'm using
normalize.quantiles(x,copy=TRUE)to do quantile normalization, but they didn't explain that, it's normalize by row or column. do you know useful function for quantile normalization?
The only other one that I know of off-hand (aside from tweaked versions, like cqn) is
limmapackage. I wouldn't be surprised if there are others.