Hi Dana, We ever released an R package that can remove probes from cdf environment, which is at http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#ProbeFilter Some peoples have tested it and it seems there is no glitch. Best, Manhong Dai > Hello, > I am trying to remove individual probes from analysis by using code > posted by Ariel Chernomoretz and modified by Jenny Drnevich. I have > a list of individual probes that I would like to remove in a tab- > delimited text file (called rejectedprobes) and the file is in my > working directory. The columns in the rejectedprobes file correspond > to and are named exactly as in the CDF file. However, when I try to > use RemoveProbes > (listOutProbes="rejectedprobes",listOutProbeSets=NULL, cleancdf) as > directed in the original instructions, it reports the error: > Error in get(x, envir, mode, inherits) : variable "rejectedprobesat" > was not found > I am wondering if anyone can give me some clues as to ways to fix > this problem. If you need more information about the problem I'm > experiencing, please let me know. > > Thanks, > Dana > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 44, Issue 28 > ********************************************

No - not a typo. By putting in 'listOutProbes="rejectedprobes"', RemoveProbes considers 'rejectedprobes' to be the name of the probe to be removed, and an internal function tries to split the number from the name, and in the course of doing so adds 'at' to the end of the probe name. The error then occurs because there is no probe named 'rejectedprobesat'. Jenny At 09:51 AM 10/30/2006, michael watson \(IAH-C\) wrote: >Looks like "rejectedprobesat" should be "rejectedprobeset" to me - typo in >the function? > >________________________________ > >From: bioconductor-bounces at stat.math.ethz.ch on behalf of Manhong Dai >Sent: Mon 30/10/2006 2:15 PM >To: bioconductor at stat.math.ethz.ch; djsomers at wisc.edu >Subject: Re: [BioC] Bioconductor Digest, Vol 44, Issue 28 > > > >Hi Dana, > > We ever released an R package that can remove probes from cdf >environment, which is at >http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#ProbeFilter > > Some peoples have tested it and it seems there is no glitch. > >Best, >Manhong Dai > > > Hello, > > I am trying to remove individual probes from analysis by using code > > posted by Ariel Chernomoretz and modified by Jenny Drnevich. I have > > a list of individual probes that I would like to remove in a tab- > > delimited text file (called rejectedprobes) and the file is in my > > working directory. The columns in the rejectedprobes file correspond > > to and are named exactly as in the CDF file. However, when I try to > > use RemoveProbes > > (listOutProbes="rejectedprobes",listOutProbeSets=NULL, cleancdf) as > > directed in the original instructions, it reports the error: > > Error in get(x, envir, mode, inherits) : variable "rejectedprobesat" > > was not found > > I am wondering if anyone can give me some clues as to ways to fix > > this problem. If you need more information about the problem I'm > > experiencing, please let me know. > > > > Thanks, > > Dana > > > > > > > > ------------------------------ > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > End of Bioconductor Digest, Vol 44, Issue 28 > > ******************************************** > >_______________________________________________ >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 > >_______________________________________________ >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

Looks like "rejectedprobesat" should be "rejectedprobeset" to me - typo in the function? ________________________________ From: bioconductor-bounces@stat.math.ethz.ch on behalf of Manhong Dai Sent: Mon 30/10/2006 2:15 PM To: bioconductor at stat.math.ethz.ch; djsomers at wisc.edu Subject: Re: [BioC] Bioconductor Digest, Vol 44, Issue 28 Hi Dana, We ever released an R package that can remove probes from cdf environment, which is at http://arrayanalysis.mbni.med.umich.edu/MBNIUM.html#ProbeFilter Some peoples have tested it and it seems there is no glitch. Best, Manhong Dai > Hello, > I am trying to remove individual probes from analysis by using code > posted by Ariel Chernomoretz and modified by Jenny Drnevich. I have > a list of individual probes that I would like to remove in a tab- > delimited text file (called rejectedprobes) and the file is in my > working directory. The columns in the rejectedprobes file correspond > to and are named exactly as in the CDF file. However, when I try to > use RemoveProbes > (listOutProbes="rejectedprobes",listOutProbeSets=NULL, cleancdf) as > directed in the original instructions, it reports the error: > Error in get(x, envir, mode, inherits) : variable "rejectedprobesat" > was not found > I am wondering if anyone can give me some clues as to ways to fix > this problem. If you need more information about the problem I'm > experiencing, please let me know. > > Thanks, > Dana > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 44, Issue 28 > ******************************************** _______________________________________________ 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