PCA to remove batch effect.
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@fabrice-tourre-4394
Last seen 10.3 years ago
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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@richard-friedman-513
Last seen 10.3 years ago
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. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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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. >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor > >
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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. >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >>
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When using ComBat, it need to know the batch effect first. Thanks. On Wed, Dec 14, 2011 at 12:29 AM, Richard Friedman <friedman at="" cancercenter.columbia.edu=""> wrote: > Rich
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Dear Fabrice, As I recall you label the input samples by batches (dates of processing) and the program takes care of the rest. Best wishes, Rich On Dec 13, 2011, at 11:33 AM, Fabrice Tourre wrote: > When using ComBat, it need to know the batch effect first. > > Thanks. > > On Wed, Dec 14, 2011 at 12:29 AM, Richard Friedman > <friedman at="" cancercenter.columbia.edu=""> wrote: >> Rich
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ComBat is now part of the sva package, so it hosts both batch correction effects. Kasper On Tue, Dec 13, 2011 at 11:35 AM, Richard Friedman <friedman at="" cancercenter.columbia.edu=""> wrote: > Dear Fabrice, > > ? ? ? ?As I recall you label the input samples by batches (dates of > processing) > and the program takes care of the rest. > > Best wishes, > Rich > > > On Dec 13, 2011, at 11:33 AM, Fabrice Tourre wrote: > >> When using ComBat, it need to know the batch effect first. >> >> Thanks. >> >> On Wed, Dec 14, 2011 at 12:29 AM, Richard Friedman >> <friedman at="" cancercenter.columbia.edu=""> wrote: >>> >>> Rich > > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor
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effects = methods On Tue, Dec 13, 2011 at 11:49 AM, Kasper Daniel Hansen <kasperdanielhansen at="" gmail.com=""> wrote: > ComBat is now part of the sva package, so it hosts both batch > correction effects. > > Kasper > > On Tue, Dec 13, 2011 at 11:35 AM, Richard Friedman > <friedman at="" cancercenter.columbia.edu=""> wrote: >> Dear Fabrice, >> >> ? ? ? ?As I recall you label the input samples by batches (dates of >> processing) >> and the program takes care of the rest. >> >> Best wishes, >> Rich >> >> >> On Dec 13, 2011, at 11:33 AM, Fabrice Tourre wrote: >> >>> When using ComBat, it need to know the batch effect first. >>> >>> Thanks. >>> >>> On Wed, Dec 14, 2011 at 12:29 AM, Richard Friedman >>> <friedman at="" cancercenter.columbia.edu=""> wrote: >>>> >>>> Rich >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor
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Kasper, I know if the batch effect is known. We can use Combat to get the new expression index without batch effect. But if the batch effect is unknown, it seems that sva can not give the new expression index without batch effect. In the example of SVA document, sva first get svobj$sv (surrogate variables), then using it in the f.test. How can we output the new expression index without batch effect? Can we use PCs(principal components) to replace surrogate variables? Sorry for this basic questions. On Wed, Dec 14, 2011 at 12:49 AM, Kasper Daniel Hansen <kasperdanielhansen at="" gmail.com=""> wrote: > ComBat is now part of the sva package, so it hosts both batch > correction effects. > > Kasper > > On Tue, Dec 13, 2011 at 11:35 AM, Richard Friedman > <friedman at="" cancercenter.columbia.edu=""> wrote: >> Dear Fabrice, >> >> ? ? ? ?As I recall you label the input samples by batches (dates of >> processing) >> and the program takes care of the rest. >> >> Best wishes, >> Rich >> >> >> On Dec 13, 2011, at 11:33 AM, Fabrice Tourre wrote: >> >>> When using ComBat, it need to know the batch effect first. >>> >>> Thanks. >>> >>> On Wed, Dec 14, 2011 at 12:29 AM, Richard Friedman >>> <friedman at="" cancercenter.columbia.edu=""> wrote: >>>> >>>> Rich >> >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor
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