Hi Pan, I was wondering, do you have a plan to release a nuID indexed annotation mapping for the Rat for BioC release 2.3? e.g., lumiRatIDMapping.db' RE: I did not see an equivalent, 'lumiRatIDMapping.db' package on the devel site for BioC 2.3 or am I wrong? * http://www.bioconductor.org/packages/2.3/data/annotation/ Thank you, ... Elliot Pan Du wrote: > Hi Elliot, > > You can find the Illumina ID mapping packages, lumiHumanIDMapping.db and > lumiMouseIDMapping.db, in the Bioc 2.3 (Developing). These packages include > all types of Illumina IDs and corresponding nuIDs. To do ID mapping, you > also need to update the lumi package to the developing version lumi 1.7.23. > Please read the vignette "IlluminaAnnotation.pdf" before using them. All > these packages can be installed and ran in R 2.7 or above. If you are using > R 2.7, you need to manually download and install them, biocLite cannot > install developing version packages. > Tell me if you have any questions. > > > Pan > > > > On 9/23/08 5:00 AM, "bioconductor-request at stat.math.ethz.ch" > <bioconductor-request at="" stat.math.ethz.ch=""> wrote: > > >> Message: 3 >> Date: Tue, 23 Sep 2008 00:39:50 -0700 >> From: Elliot Kleiman <kleiman at="" rohan.sdsu.edu=""> >> Subject: [BioC] How to convert Illumina ProbeIDs to nuIDs without nuID >> indexed annotation libraries? >> To: bioconductor at stat.math.ethz.ch >> Message-ID: <48D89D46.2050405 at rohan.sdsu.edu> >> Content-Type: text/plain; charset=ISO-8859-1; format=flowed >> >> Hi BioC, >> >> [Question]: >> * How do you convert Illumina ProbeIDs to nuIDs without nuID >> indexed annotation libraries? >> >> i.e., >> >> ... the following previous BioC 2.1 released nuID indexed annotation >> libraries, >> >> * lumiRatV1 >> * lumiMouseV1 >> * lumiHumanV1 >> * lumiHumanV2 >> >> ... are not available in BioC release 2.2, >> * http://www.bioconductor.org/packages/2.2/data/annotation/ >> >> RE: My objective is to map probeIDs to nuIDs standalone without >> first having to create a lumiBatch object via the lumi package. >> >> There is a new annotation package, 'lumiRatAll.db' in BioC 2.2, >> but it doesn't provide the functional mapping of ProbeIDs to nuIDs; >> it assumes you already have nuIDs. >> >> e.g., >> The lumi package offers a function that can map Illumina probeIDs >> to nuIDs, 'probeID2nuID()'. But the problem is that it requires >> a 'lib' argument to specify a nuID indexed annotation library >> (none of which are currently available in the current 2.2 release). >> * http://www.bioconductor.org/packages/2.2/data/annotation/ >> >> e.g., >> >> # load lumi package from BioC release 2.2 >> >>> library(lumi) >>> >> # get help on lumi function probeID2nuID >> >>> help(probeID2nuID) >>> >> Print-out excerpt of help documentation for function >> 'probeID2nuID()' from package 'lumi', >> >> # probeID2nuID package:lumi R Documentation >> # Usage: >> # probeID2nuID(probeID, lib = "lumiHumanV1") >> # Arguments: >> # probeID: a vector of Illumina ProbeID >> # lib: a nuID indexed Illumina annotation library >> >> e.g. >> # Not Run b/c no annotation libs loaded b/c they aren't available to install >> >>> nu <- probeID2nuID(pid, lib = "lumiHumanV1") >>> >> Am I [like totally] missing something here? >> >> Thanks, >> >> ... Elliot >> >> >>> # print sessionInfo() >>> sessionInfo() >>> >> R version 2.7.2 (2008-08-25) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=C;LC_MONETARY= C;LC_MESSAG >> ES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_ME ASUREMENT=e >> n_US;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] splines tools stats graphics grDevices utils datasets >> [8] methods base >> >> other attached packages: >> [1] illuminaRatv1ProbeID.db_1.1.1 GOstats_2.6.0 >> [3] Category_2.6.0 genefilter_1.20.0 >> [5] survival_2.34-1 RBGL_1.16.0 >> [7] GO.db_2.2.0 graph_1.18.1 >> [9] lumiRatAll.db_1.2.0 lumi_1.6.2 >> [11] mgcv_1.4-1 beadarray_1.8.0 >> [13] affy_1.18.2 preprocessCore_1.2.1 >> [15] affyio_1.8.1 geneplotter_1.18.0 >> [17] annotate_1.18.0 xtable_1.5-3 >> [19] AnnotationDbi_1.2.2 RSQLite_0.7-0 >> [21] DBI_0.2-4 lattice_0.17-14 >> [23] Biobase_2.0.1 limma_2.14.6 >> >> loaded via a namespace (and not attached): >> [1] KernSmooth_2.22-22 RColorBrewer_1.0-2 cluster_1.11.11 >> grid_2.7.2 >> [5] tcltk_2.7.2 >> >> -- >> __________________________ >> MS graduate student >> Program in Computational Science >> San Diego State University >> http://www.csrc.sdsu.edu/ >> http://www.rohan.sdsu.edu/~kleiman/ >> >> > > > > > -- __________________________ MS graduate student Program in Computational Science San Diego State University http://www.csrc.sdsu.edu/