[BioC] PCA to remove batch effect.

[Fabrice Tourre]

Dear Rich,

Thank you for your suggestions.

In their paper, the suggested using sva.

I have try sva, but it seems that SVA cannot output the new expression
index without batch effect.

Thank you

On Tue, Dec 13, 2011 at 10:51 PM, Richard Friedman
<friedman at cancercenter.columbia.edu> wrote:
> 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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>
>