Hi everyone,

We had been working on analyzing some Affymetrix gene chip data (mogene 1.0
st and hugene 1.0 st), and saw quite a few chips with intensity-dependent
bias. These chips, after rma normalization using package oligo, give s-shape
MA plots. We've tried xps package as well, but it doesn't seem to have loess
normalization implemented for Affy GeneChip.

So we're wondering if there's other packages/functions that can normalize
Affymetrix gene chips using other methods, such as loess?

Thanks in advance!


-- 
Bin Ye

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