Dear mailing list, I would like to use nuIDs for Affymetrix and Agilent probes. Is there a way to accomplish this? What would I have to do to get a nuID mapping of Affymetrix and Agilent probes? Thanks in advance, Andreas Heider [[alternative HTML version deleted]]

On Wed, Aug 10, 2011 at 11:27 AM, Andreas Heider <aheider at="" trm.uni-leipzig.de=""> wrote: > Dear mailing list, > I would like to use nuIDs for Affymetrix and Agilent probes. Is there a way > to accomplish this? What would I have to do to get a nuID mapping of > Affymetrix and Agilent probes? Hi, Andreas. You would need the actual nucleotide sequences and the seq2id() function in the lumi package. However, I'm not sure how useful that will be to you since annotation packages are typically based on platform identifiers, so you would need to build your own annotation packages to support the annotation Pan has built into lumi. Sean

Yes, you are right. I can convert probe sequences into nuIDs easily. But the author of lumi has done a mapping of the probe sequences to the RefSeq database and made a annotation package that maps Illumina nuIDs to whatever Identifier. I want to have a consistent annotation for several chips and I think the probe sequence is most reliable as all other identifiers have flaws such as some missing and some multiple hits. 2011/8/10 Freudenberg, Johannes (NIH/NIEHS) [E] < johannes.freudenberg@nih.gov> > Hi Andreas, > > Not sure if it helps but this website > https://prod.bioinformatics.northwestern.edu/nuID/index.cfm supposedly > offers "a number of tools, software downloads, and data sets for working > with nuIDs..." Seems like you can easily generate nuIDs with these tools if > you have the probe sequences. > > Viele Gruese nach Leipzsch! > --Johannes > > > > -----Original Message----- > From: Andreas Heider [mailto:aheider@trm.uni-leipzig.de] > Sent: Wednesday, August 10, 2011 11:27 AM > To: mailman, bioconductor > Subject: [BioC] lumi package, nuIDs and Agilent, Affymetrix > > Dear mailing list, > I would like to use nuIDs for Affymetrix and Agilent probes. Is there a way > to accomplish this? What would I have to do to get a nuID mapping of > Affymetrix and Agilent probes? > > Thanks in advance, Andreas Heider > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]