I'm working through a paper and it mentions: "[After RMA normalization] ...each gene on the treatment sample arrays were normalised to the median signal intensity of the of the respective gene on the control array."
I'm thinking of using
normalizeBetweenArrays (if that's even the correct function to use?) which takes
a numeric matrix, EListRaw, RGList or MAList object containing un-normalized expression data.
But what I have is an expressionSet object.
How would I do this in Limma?