[BioC] PCA to remove batch effect.

[Richard Friedman]

Dear Fabrice,

	The following paper from Rafael Irizarry's lab will tell you what you  
need to know:

http://www.ncbi.nlm.nih.gov/pubmed/20838408
  Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE,  
Geman D, Baggerly K, Irizarry RA. Tackling the widespread and critical  
impact of batch effects in high-throughput data. Nat Rev Genet. 2010  
Oct;11(10):733-9. Epub 2010 Sep 14.
  PubMed PMID: 20838408.

Best wishes,
Rich


On Dec 13, 2011, at 9:45 AM, Fabrice Tourre wrote:

> Dear list,
>
> In my mrcroarray data, there is batch effect. But I am not very clear
> what kind of batch effect in it. I want to using PCA to remove batch
> effect, but I am confused how to from the raw expression data to get a
> new expression data without batch effect in it.
>
> Any suggestion will be welcome.
>
> Thanks.
>
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