[BioC] Affymetrix Gene Chip Normalization
okko at clevert.de
Thu Jun 23 17:01:53 CEST 2011
try to use lFarms in the farms package to process your
arrays with loess normalization and farms summarization.
dipl.-inf. djork clevert | gleimstr. 13a | d-10437 berlin
e: okko at clevert.de
p: +49.30.4432 4702
f: +49.30.6883 5307
Am 23.06.2011 um 14:55 schrieb Bin Ye:
> 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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