An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20071214/ b388c5cf/attachment.pl

I cannot speak to lumiHumanV1 content but the illuminaHumanv1 package is made by searching NCBI databases for RefSeq identifiers provided by Illumina for each Illumina 'Target' identifier. In future releases, I will provide an alternative package based on the probe identifiers written out by the scanner. Also, in the next release I will blast the probe sequences and only include those with perfect matches to an exonic region. Lynn burak kutlu wrote: > Hi > Is there a difference between illuminaHumanv1 and lumiHumanV1 packages in terms of content? > Thanks a lot > -burak > > > > ______________________________________________________________ ______________________ > Never miss a thing. Make Yahoo your home page. > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 >

Hi Burak > Is there a difference between illuminaHumanv1 and lumiHumanV1 packages in terms of content? > Thanks a lot > -burak Here is the situation afaiCs for illuminaHumanv2 and lumiHumanV2 packages: - in lumiHumanV2, annotation environments are indexed by Pan Du's nuID [1], which correspond 1:1 to reporter sequence IDs, and a translation table is provided to Illumina *Probe* IDs. AfaIu, the package authors do their own mapping of reporter sequences to the transcriptome. - in illuminaHumanv2, annotation environments are indexed by the Illumina *target* ID, which correspond to the intended (by Illumina) target gene. See Lynn's message. With the current package version 1.4.0., the function illuminaHumanv2() returns strange "quality control" results about "Probe number missmatch". In both cases, I have not found documentation of the quality and uniqueness of the matches of the reporters to the transcriptome. [1] Du, P., Kibbe, W.A. and Link, S.M., "nuID: A universal naming schema of oligonucleotides for Illumina, Affymetrix, and other microarrays", submitted. Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber