[BioC] Integration of different microarray data (same platform)

Matthew McCall mccallm at gmail.com
Thu Oct 24 14:59:42 CEST 2013

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.


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.
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Matthew N McCall, PhD
112 Arvine Heights
Rochester, NY 14611
Cell: 202-222-5880

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