Dear all, I made a pipeline to analyse Illumina beadarray. I tried to install my pipeline in a new computer. I use a filter based on the illuminaHumanv4PROBEQUALITY function of the illuminaHumanv4.db package. In the new computer this step don't work because some id are missing. I found that the problem comes from illuminaHumanv4ARRAYADDRESS function that I need to get Illumina "PROBE_ID" (ILMN_XXX) from the "probeID". There is 48107 "probeID" but only 48070 "PROBE_ID". In an older version there is 48107" probeID" and "PROBE_ID". For example the "PROBE_ID" for the 2030348 is missing. IlluminaHumanv4.db is valuable package so I would like to keep using it. What Can I do? > length(illuminaHumanv4ARRAYADDRESS) => 48107 > length(revmap(illuminaHumanv4ARRAYADDRESS)) => 48070 This is my first message in the bioconductor list. Please tell me if I did something wrong. Thank you very much. Best regards Amos Kirilovsky Dr. Amos Kirilovsky INSERM UMR-S 945 Institut fédératif de Recherches (IFR) 113 : Immunité-Cancer- Infection Hôpital Pitié-Salpêtrière 75651 PARIS Cedex 13 Direct Line : 33-1-42-17-7521 Secretary : 33-1-42-17-74-81 [[alternative HTML version deleted]]

Hi Amos, This package was contributed by Mark Dunning. I am fairly confident that he probably had good reasons for removing some of the probes from it, but I can't speak for him. You also always have the option of making a package yourself by following the instructions in the SQLForge vignette (which can be found here). http://www.bioconductor.org/packages/2.10/bioc/vignettes/AnnotationDbi /inst/doc/SQLForge.pdf To make use of this, you simply need the information from the manufacturer about which probe IDs map to which genes and from that information, you can generate one. However, this particular package also contains some "extra" information (which it seems like you might be using), and to make use of that requires a little more work. Specifically you will need dot make use of the createSimpleBimap() function, and you will also need to add some extra information into the database (beyond what will be done for you). Marc On 07/18/2012 03:43 AM, Amos Kirilovsky wrote: > Dear all, > > I made a pipeline to analyse Illumina beadarray. I tried to install my > pipeline in a new computer. I use a filter based on the > illuminaHumanv4PROBEQUALITY function of the illuminaHumanv4.db package. In > the new computer this step don't work because some id are missing. I found > that the problem comes from illuminaHumanv4ARRAYADDRESS function that I > need to get Illumina "PROBE_ID" (ILMN_XXX) from the "probeID". There is > 48107 "probeID" but only 48070 "PROBE_ID". In an older version there is > 48107" probeID" and "PROBE_ID". > For example the "PROBE_ID" for the 2030348 is missing. IlluminaHumanv4.db > is valuable package so I would like to keep using it. What Can I do? > >> length(illuminaHumanv4ARRAYADDRESS) > => 48107 >> length(revmap(illuminaHumanv4ARRAYADDRESS)) > => 48070 > > This is my first message in the bioconductor list. Please tell me if I did > something wrong. > > Thank you very much. > Best regards > Amos Kirilovsky > > > > Dr. Amos Kirilovsky > INSERM UMR-S 945 > Institut fédératif de Recherches (IFR) 113 : Immunité-Cancer- Infection > Hôpital Pitié-Salpêtrière > 75651 PARIS Cedex 13 > Direct Line : 33-1-42-17-7521 > Secretary : 33-1-42-17-74-81 > > [[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]]