[BioC] affy: batch completely confounded with treatment

[Matthew McCall]

Juliet,

You could use fRMA, which down-weights probes that are particular
susceptible to batch-effects, to preprocess the data.

Paper:
McCall MN, Bolstad BM, and Irizarry RA* (2010). Frozen Robust
Multi-Array Analysis (fRMA), Biostatistics, 11(2):242-253.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830579/

BioC package vignette:
http://bioconductor.org/packages/devel/bioc/vignettes/frma/inst/doc/frma.pdf

Best,
Matt


On Mon, Aug 13, 2012 at 2:46 PM, Juliet Hannah <juliet.hannah at gmail.com> wrote:
> All,
>
> A collaborator has approached me with a situation in which a batch is
> completely confounded with treatment for
> affy gene expression data.
>
> I am wondering if there is anything reasonable to try? For example,
> I'm wondering if anything can be done with
> control genes.
>
> Does anyone have any suggestions, pointers to papers, or a template
> script? The key feature is, of course, the complete
> confounding, so that it seems Combat or SVA are not applicable
> (correct me if this is incorrect).
>
> I am looking for a way to use the data to generate hypotheses and make
> some guesses
> with these limitations.
>
> Thanks,
>
> Juliet
>
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Matthew N McCall, PhD
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