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

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 > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor Search the > archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- 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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues