I need to integrate affymetrix data from different labs into one large expression matrix. This matrix will have different experiments as the columns and genes as rows. How can I do this in a way that is statistically robust. Should I normalize each experiment individually and column bind all the different experiments? Thanks! -- output of sessionInfo(): R version 3.0.1 (2013-05-16) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.10.4 loaded via a namespace (and not attached): [1] Biobase_2.20.1 BiocGenerics_0.6.0 parallel_3.0.1 tools_3.0.1 -- Sent via the guest posting facility at bioconductor.org.

Have a look at the frma package and paper: McCall MN, Bolstad BM, and Irizarry RA (2010). Frozen Robust Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253. And maybe the barcode paper as well (also implemented in the frma packge): McCall MN, Uppal K, Jaffee HA, Zilliox MJ, and Irizarry RA (2011). The Gene Expression Barcode: leveraging public data repositories to begin cataloging the human and murine transcriptomes, Nucleic Acids Research, 39:D1011-5. Best, Matt On Wed, Oct 23, 2013 at 11:57 PM, Chirag Gupta [guest] <guest at="" bioconductor.org=""> wrote: > > I need to integrate affymetrix data from different labs into one large expression matrix. This matrix will have different experiments as the columns and genes as rows. How can I do this in a way that is statistically robust. Should I normalize each experiment individually and column bind all the different experiments? > > Thanks! > > -- output of sessionInfo(): > > R version 3.0.1 (2013-05-16) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.10.4 > > loaded via a namespace (and not attached): > [1] Biobase_2.20.1 BiocGenerics_0.6.0 parallel_3.0.1 tools_3.0.1 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 -- Matthew N McCall, PhD 112 Arvine Heights Rochester, NY 14611 Cell: 202-222-5880