[BioC] Replacing an AffyBatch probe set

James W. MacDonald jmacdon at med.umich.edu
Fri Jul 9 23:14:56 CEST 2010


Hi Eli,

On 7/9/2010 2:48 PM, Eli Moss wrote:
> Hello All,
>
> I am an undergrad at Brown University looking at Drosophila
> microarrays.  I am developing a new method of removing SNP's detected
> in probe-level intensity values, but I am having trouble getting the
> modified probe set back into the affybatch object in such a way that
> subsequent bioconductor actions then work on it.  Any ideas?

This might be of some help:

https://stat.ethz.ch/pipermail/bioconductor/2006-September/014242.html

Best,

Jim


>
> affy.object = readAffy() affy.object.normalized =
> normalize(affy.object) probes = probeset(affy.object.normalized)
> probes = [probes are modified here, retaining their structure]
> assayData(affy.object.normalized) = probes
>
> ...then when I try to call rma(affy.object.normalized), it crashes,
> saying:
>
> Background correcting Error in rma(affy.object.normalized) :
> INTEGER() can only be applied to a 'integer', not a 'NULL'
>
>
> trying a mas5 normalization crashes R completely with a non-existent
> physical address bus error.
>
> How can I replace the probe intensity data in an AffyBatch object
> with the modified matrix I got from a call to probeset()?
>
> Thank you, Eli
>
>
>
> -- Eli Moss Brown University, Computational Biology +1 (413)
> 658-4227 Eli_Moss at Brown.edu
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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