crlmm Illumina cdfName "human1mv1c" not valid
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@richard-thompson-5371
Last seen 7.1 years ago
Hi Everyone, I was really hoping someone could help me with this; I've tried searching to no avail, however I apologise if something similar has been discussed before. I'm trying to use crlmm to carry out LOH and CNV analysis based on .idat files created using the Illumina 1M bead chips. I'm sure I've got it installed correctly (I'm new to Bioconductor, but I've been using R for years) and I've double-checked all my steps, but I can't seem to get past this problem. Under both my normal installation and vanilla, when I run: crlmmIlluminaV2(sampleSheet=samplesheet,arrayNames=arrayNames,arrayInf oColNames=list(barcode=NULL,position="Sentrix_Position"),cdfName="huma n1mv1c",saveDate=TRUE,returnParams=TRUE,path=".") I'm getting: Error in crlmmIlluminaV2(sampleSheet = samplesheet, arrayNames = arrayNames, : cdfName not valid. see validCdfNames In addition: Warning message: In isValidCdfName(cdfName) : cdfName must be one of the following: genomewidesnp6genomewidesnp5human370v1chuman370quadv3chuman550v3bhuman 650v3ahuman610quadv1bhuman660quadv1ahuman1mduov3bhumanomni1quadv1bhuma nomniexpress12v1bhumanomni25quadv1bhumanimmuno12v1bhumancytosnp12v2p1h ..even though the reference states that it is valid for other functions. Can anyone give me any suggestion why this may be happening and/or how I can get this to work? Many Thanks Richard Thompson > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-redhat-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] cacheSweave_0.6-1 stashR_0.3-5 filehash_2.2-1 [4] ff_2.2-7 bit_1.1-8 crlmm_1.14.2 [7] oligoClasses_1.18.0 loaded via a namespace (and not attached): [1] affyio_1.24.0 annotate_1.34.1 AnnotationDbi_1.18.1 [4] Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.7 [7] Biostrings_2.24.1 codetools_0.2-8 DBI_0.2-5 [10] digest_0.5.2 ellipse_0.3-7 foreach_1.4.0 [13] genefilter_1.38.0 grid_2.15.0 IRanges_1.14.3 [16] iterators_1.0.6 lattice_0.20-6 mvtnorm_0.9-9992 [19] preprocessCore_1.18.0 RSQLite_0.11.1 splines_2.15.0 [22] stats4_2.15.0 survival_2.36-14 XML_3.9-4 [25] xtable_1.7-0 zlibbioc_1.2.0 > [[alternative HTML version deleted]]
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Rob Scharpf ▴ 250
@rob-scharpf-1931
Last seen 7.1 years ago
Hi Richard, This is a bug. I checked in a fix for release version 1.14.3. Both of the following should evaluate to TRUE crlmm:::isValidCdfName("human1mv1c") crlmm:::isValidCdfName("human1mv1cCrlmm") thanks- Rob On Jul 1, 2012, at 1:36 PM, Richard Thompson wrote: > Hi Everyone, > > I was really hoping someone could help me with this; I've tried > searching to no avail, however I apologise if something similar has been > discussed before. > > I'm trying to use crlmm to carry out LOH and CNV analysis based on .idat > files created using the Illumina 1M bead chips. > > I'm sure I've got it installed correctly (I'm new to Bioconductor, but > I've been using R for years) and I've double-checked all my steps, but I > can't seem to get past this problem. Under both my normal installation > and vanilla, when I run: > > crlmmIlluminaV2(sampleSheet=samplesheet,arrayNames=arrayNames,arrayI nfoColNames=list(barcode=NULL,position="Sentrix_Position"),cdfName="hu man1mv1c",saveDate=TRUE,returnParams=TRUE,path=".") > > I'm getting: > > Error in crlmmIlluminaV2(sampleSheet = samplesheet, arrayNames = > arrayNames, : > cdfName not valid. see validCdfNames > In addition: Warning message: > In isValidCdfName(cdfName) : > cdfName must be one of the following: > genomewidesnp6genomewidesnp5human370v1chuman370quadv3chuman550v3bhum an650v3ahuman610quadv1bhuman660quadv1ahuman1mduov3bhumanomni1quadv1bhu manomniexpress12v1bhumanomni25quadv1bhumanimmuno12v1bhumancytosnp12v2p 1h > > ..even though the reference states that it is valid for other functions. > Can anyone give me any suggestion why this may be happening and/or how I > can get this to work? > > Many Thanks > Richard Thompson > >> sessionInfo() > R version 2.15.0 (2012-03-30) > Platform: x86_64-redhat-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.utf8 LC_NUMERIC=C > [3] LC_TIME=en_GB.utf8 LC_COLLATE=en_GB.utf8 > [5] LC_MONETARY=en_GB.utf8 LC_MESSAGES=en_GB.utf8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C > > attached base packages: > [1] tools stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] cacheSweave_0.6-1 stashR_0.3-5 filehash_2.2-1 > [4] ff_2.2-7 bit_1.1-8 crlmm_1.14.2 > [7] oligoClasses_1.18.0 > > loaded via a namespace (and not attached): > [1] affyio_1.24.0 annotate_1.34.1 AnnotationDbi_1.18.1 > [4] Biobase_2.16.0 BiocGenerics_0.2.0 BiocInstaller_1.4.7 > [7] Biostrings_2.24.1 codetools_0.2-8 DBI_0.2-5 > [10] digest_0.5.2 ellipse_0.3-7 foreach_1.4.0 > [13] genefilter_1.38.0 grid_2.15.0 IRanges_1.14.3 > [16] iterators_1.0.6 lattice_0.20-6 mvtnorm_0.9-9992 > [19] preprocessCore_1.18.0 RSQLite_0.11.1 splines_2.15.0 > [22] stats4_2.15.0 survival_2.36-14 XML_3.9-4 > [25] xtable_1.7-0 zlibbioc_1.2.0 >> > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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