Cindy, apologies for my previous email, please ignore it, as I rolled oligo back to 1.18.1 (this is the oligo released for BioC 2.9, which is no longer built, so you won't benefit from it at all). You should wait for the release of BioC 2.10 and use it instead. The issue you reported is fixed there. Apologies for any inconvenience, benilton On 30 March 2012 11:01, Benilton Carvalho <beniltoncarvalho@gmail.com>wrote: > Thank you very much for the report. > > Issue fixed on oligo 1.18.2... which may become available in 1 or 2 > days... Note that a new BioC (v 2.10) will be released very very soon and > this issue is already addressed for the new release as well. > > Thanks, benilton > > On 30 March 2012 04:02, Cindy [guest] <guest@bioconductor.org> wrote: > >> >> Dear Bioconductor team, >> >> I am currently using the oligo package for analyzing tiling array data >> (Affymetrix GeneChip Human Tiling 2.0R Array). I made a PlatformDesign >> package (pd.hs35b.p02r.v01_0.0.1) using the makePdInfoPackage function from >> pdInfoBuilder package. The .bpmap file used to make this package was >> downloaded from the Affymetrix website at >> http://www.affymetrix.com/analysis/downloads/lf/tiling/Hs35b_PR_v01 -3_NCBIv36.bpmap.zip >> >> seed <- new( >> "AffyTilingPDInfoPkgSeed", >> bpmapFile = bpmap, >> celFile = celfile, >> author = "Cindy Yao", >> biocViews = "AnnotationData", >> genomebuild = "NCBI Build 36", >> organism = "Human", >> species = "Homo Sapiens" >> ); >> >> # create package >> makePdInfoPackage(seed, destDir = cfg$platform.design.directory); >> >> I was able to read in the cel files using the read.celfiles; however, I >> came across a problem when I try to extract information about the probe >> position, sequence and which chromosome it belongs to. It appears that the >> length of the chromosome vector doesn't equal to the length of the position >> vector and the number of rows from the intensity data. The code that I used >> is displayed below as well as the respective structures of each object: >> >> data <- read.celfiles(ArrayFiles); >> >> pm.data <- pm(data); >> pm.chr <- pmChr(data); >> pm.position <- pmPosition(data); >> >> str(pm.data) >> num [1:6003165, 1:10] 56 73 155 98 60 103 91 184 176 110 ... >> - attr(*, "dimnames")=List of 2 >> ..$ : chr [1:6003165] "2566" "2567" "2568" "2569" ... >> ..$ : chr [1:10] "1_10_(Hs35b_P02R_v01).CEL" "1_11_(Hs35b_P02R_v01).CEL" >> "1_12_(Hs35b_P02R_v01).CEL" "1_13_(Hs35b_P02R_v01).CEL" ... >> >> str(pm.chr) >> chr [1:6002540] "chr2" "chr9" "chr2" "chr2" "chr9" "chr9" ... >> >> str(pm.position) >> int [1:6003165] 80928567 125675126 6587123 22535130 20912500 118746438 >> 138140160 130174378 202638022 133066609 ... >> >> I am not sure where the problem is. Could someone help me out? Thank you >> very much for your time! >> >> Best, >> Cindy >> >> -- output of sessionInfo(): >> >> R version 2.14.2 (2012-02-29) >> Platform: x86_64-unknown-linux-gnu (64-bit) >> >> locale: >> [1] C >> >> attached base packages: >> [1] stats graphics grDevices datasets methods utils base >> >> other attached packages: >> [1] pd.hs35b.p02r.v01_0.0.1 RSQLite_0.11.1 DBI_0.2-5 >> [4] affxparser_1.26.4 oligo_1.18.1 oligoClasses_1.16.0 >> [7] Biobase_2.14.0 >> >> loaded via a namespace (and not attached): >> [1] Biostrings_2.22.0 IRanges_1.12.6 affyio_1.22.0 >> [4] bit_1.1-8 ff_2.2-5 preprocessCore_1.16.0 >> [7] splines_2.14.2 tools_2.14.2 zlibbioc_1.0.1 >> >> -- >> Sent via the guest posting facility at bioconductor.org. >> >> _______________________________________________ >> 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]]