[BioC] multi-experiment multi-chip summarization

[Henrik Bengtsson]

On Jan 30, 2008 4:04 AM, Anna Lobley <A.Lobley at cs.ucl.ac.uk> wrote:
> I am trying to integrate several diverse affy datasets
> from the GEO database all from the same organism
> same chip design (~500 samples).
>
> I'm interested in obtaining absolute expression values
> and have created a robust target distribution for quantile normalisation
> over all samples (carried out externally from R).
>
> Due to cpu memory requirements I have only
> been able to run median polish for probe summarization on the dataset
> within single GEO experiments rather than across all of the quantile
> normalised data in one go.
>
> My question is fairly open ended and as follows:
> I'm concerned that this methodology will over-emphasize
> variance between experiments that could be avoided using
> median polish over the entire dataset. Is there a more
> appropriate way of carrying out summarization on this large
> dataset?

If you've got your data as CEL files with a corresponding CDF file,
you could try the aroma.affymetrix package:

  http://www.braju.com/R/aroma.affymetrix/

/Henrik

>
> thanks in advance for opinions/help
>
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