Question

Design matrix in Combat algorithm

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I am currently trying to use ComBat from sva package in order to eliminate the batch effect from some Ilumina data obtained in an experiment. I have read the article Adjusting batch effects in microarray expression data using empirical Bayes method,W. EVAN JOHNSON, CHENG LI???,ARIEL RABINOVIC but I did not understand very well how the elements in matrix X of the model Yijg = ??g + X??g + ??ig + ??ig??ijg are obtained. Could you please give me a better insight on this subject? Thank you very much, Neagu Matei Stefan -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=Romanian_Romania.1250 LC_CTYPE=Romanian_Romania.1250 [3] LC_MONETARY=Romanian_Romania.1250 LC_NUMERIC=C [5] LC_TIME=Romanian_Romania.1250 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.

sva sva • 984 views

ADD COMMENT • link updated 10.3 years ago by W. Evan Johnson ▴ 850 • written 10.3 years ago by Guest User ★ 13k

score 0 · Answer 1 · 2014-01-22

Matei, X is a design matrix for your covariates of interest or possible confounding factors. If the covariates are categorical with k levels, then the columns of X will contain k-1 indicator variables for the different factor levels. If this still does not make sense, I would STRONGLY recommend you go talk to a statistician at your university and have her/him help you analyze your data. Thanks! Evan On Jan 22, 2014, at 6:00 AM, <bioconductor-request at="" r-project.org=""> wrote: > Date: Wed, 22 Jan 2014 02:30:33 -0800 (PST) > From: "Neagu Matei Stefan [guest]" <guest at="" bioconductor.org=""> > To: bioconductor at r-project.org, m.neagu at sheffield.ac.uk > Cc: sva Maintainer <jleek at="" jhsph.edu=""> > Subject: [BioC] Design matrix in Combat algorithm > Message-ID: <20140122103033.A57C7143D7F at mamba.fhcrc.org> > Content-Type: text/plain; charset=iso-8859-1 > > > > I am currently trying to use ComBat from sva package in order to eliminate the batch effect from some Ilumina data obtained in an experiment. I have read the article Adjusting batch effects in microarray expression data > using empirical Bayes method,W. EVAN JOHNSON, CHENG LI???,ARIEL RABINOVIC but I did not understand very well how the elements in matrix X of the model Yijg = ??g + X??g + ??ig + ??ig??ijg are obtained. > Could you please give me a better insight on this subject? > > Thank you very much, > Neagu Matei Stefan > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=Romanian_Romania.1250 LC_CTYPE=Romanian_Romania.1250 > [3] LC_MONETARY=Romanian_Romania.1250 LC_NUMERIC=C > [5] LC_TIME=Romanian_Romania.1250 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > -- > Sent via the guest posting facility at bioconductor.org.