Normalizing genes between arrays with Limma

Question

[BioinformaticsLad]

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?

Answer 1

[Gordon Smyth]

No, that is not what normalizeBetweenArrays does.

I don't follow entirely what the quoted sentence means, but it appears to be a form of standardization rather than a type of normalization. This standardization is not usual so you are not likely to find a canned funtion to do it. It would be best to give the full paper reference so that people can check exactly what was done and perhaps help you.

[BioinformaticsLad]

Thanks Gordon! It does appear that it's an uncommon procedure. I couldn't find direct references to normalizing to genes anywhere.

The authors wanted to compare the differential expression of a drug-treated cells vs. untreated control cells. Besides that sentence pasted above, they don't really go into much else detail. What would even be the point of such a standardization procedure? Wouldn't that simply decrease the level of differential expression between conditions?