[BioC] PCA to remove batch effect.

[Richard Friedman]

Dear Fabrice,

	They also recommend and give references to a program called ComBat
which removes batch effects.

Best wishes,
Rich
------------------------------------------------------------
Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Educational Coordinator,
Center for Computational Biology and Bioinformatics (C2B2)/
National Center for Multiscale Analysis of Genomic Networks (MAGNet)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
friedman at cancercenter.columbia.edu
http://cancercenter.columbia.edu/~friedman/

I am a Bayesian. When I see a multiple-choice question on a test and I  
don't
know the answer I say "eeney-meaney-miney-moe".

Rose Friedman, Age 14







On Dec 13, 2011, at 11:27 AM, Fabrice Tourre wrote:

> 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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>>
>>