Hi,

I would like to manually compute NUSE scores for Affy Microarray Data, but I do not know to do it. I computed the RLE score by subtracting its median to a matrix of intensities, but can't find a formula for NUSE.

Why not use the affyPLM package? You can find in the package's web site Ben Bolstad's publications where it is descibed. It is also described in this paper by Rafael Irizarry: Assessing affymetrix GeneChip microarray quality.