[BioC] Affymetrix Gene Chip Normalization

[Djork-Arné Clevert]

Hi Bin,

try to use lFarms in the farms package to process your 
arrays with loess normalization and farms summarization.

Cheers,
Okko
-- 

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e: okko at clevert.de
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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
> 
> 	[[alternative HTML version deleted]]
> 
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