Using the argument: pkgname="pd.mapping250k.nsp" in crlmm() should get the job done by overriding the type check. b On 28/06/2009, at 14:18, "Henrik Bengtsson" <hb at="" stat.berkeley.edu=""> wrote: > The chip types are identical - it is only the CDFs that differ. > Assuming the assays didn't change too much you should be able to > analyze them together. A workaround is to create a copy of the "old" > CEL files with an updated chip type, e.g. > > library("affxparser"); > convertCel(filename, outFilename, newChipType="Mapping250K_Nsp"); > > /Henrik > > On Sat, Jun 27, 2009 at 8:55 PM, Vincent > Carey<stvjc at="" channing.harvard.edu=""> wrote: >> Examining the platform metadata for GSE9222 we can see that there are >> "early access" Nsp arrays >> and standard 250k Nsp. I would think that your best bet is to use >> samples that are clearly from platform >> GPL3718. >> >> On Sat, Jun 27, 2009 at 6:32 PM, <mcoyne at="" boninc.com=""> wrote: >>> I downloaded a number of SNP 500K data from GEO to run with CRLMMM. >>> The following CEL files specified by GEO as NspI files. >>>> fulFileNames >>> [1] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234158.CEL" >>> [2] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234160.CEL" >>> [3] "/Users/pcoyne/B_Cluster_DBased/GSE9222/NspI/GSM234162.CEL" >>>> crlmm (fulFileNames,outputDir,verbose=TRUE, >>> pkgname="pd.mapping250k.nsp") >>> chips >>> Mapping250K_Nsp Mendel_Nsp >>> 2 1 >>> Error in justCRLMMv3(filenames, outdir, batch_size = batch_size, >>> recalibrate = recalibrate, : >>> All the CEL files must be of the same type. >>>> sessionInfo() >>> R version 2.9.0 (2009-04-17) >>> i386-apple-darwin8.11.1 >>> locale: >>> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> attached base packages: >>> [1] stats graphics grDevices utils datasets methods base >>> >>> other attached packages: >>> [1] pd.mapping250k.sty_0.4.1 pd.mapping250k.nsp_0.4.1 RSQLite_0.7-1 >>> >>> [4] DBI_0.2-4 oligo_1.8.1 >>> preprocessCore_1.6.0 >>> [7] oligoClasses_1.6.0 Biobase_2.4.1 >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.16.0 affyio_1.12.0 Biostrings_2.12.7 >>> IRanges_1.2.3 >>> [5] splines_2.9.0 >>>> >>> Question 1: What is Mendel_nsp? It looks like one of the file is >>> Mendel_nsp >>> Question 2: Is this an error that I can by pass with CRLMM and how? >>> or is it an error that I should report to GEO for fixitng? >>> Thanks >>> My Coyne >>> mcoyne at boninc.com >>> BODY { font-family:Arial, Helvetica, sans-serif;font-size:12px; } >>> [[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 >>> >> >> >> >> -- >> Vincent Carey, PhD >> Biostatistics, Channing Lab >> 617 525 2265 >> >> _______________________________________________ >> 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 >> > > _______________________________________________ > 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