[BioC] Replacing an AffyBatch probe set

[Eli Moss]

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?

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