[From nobody Thu Dec 13 10:37:52 2007 Message-ID: <4756BD46.3070404@psb.ugent.be> Date: Wed, 05 Dec 2007 16:01:26 +0100 From: Naira Naouar <nanao@psb.ugent.be> User-Agent: Thunderbird 1.5.0.8 (Windows/20061025) MIME-Version: 1.0 To: Benilton Carvalho <bcarvalh@jhsph.edu> Subject: Re: [Fwd: [BioC] Oligo package and tiling arrays - PM and MM] References: <4753D700.8030609@psb.ugent.be> <3272923C-8433-4226-ABDF-4A7BAEA98F9D@jhsph.edu> In-Reply-To: <3272923C-8433-4226-ABDF-4A7BAEA98F9D@jhsph.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Content-Transfer-Encoding: 7bit Hi Benilton, Sorry for the late reply but I wanted to check again that I did all right and I manage to reproduce the same mistake. I explain all the process here: 1. Creation of the tiling a) I am working on Arabidopsis thaliana 1.0R array so i took from affymetrix the library files (you already did it before also (see the forwarded mail following this one :) ) b) contruction of tilingcdf with makeplatformdesign package: ***** R Code **** >pwd=getwd() >extra=list(packagename="tilingcdf",cdf.path=pwd,package.path=pwd,author="Naira Naouar",maintainer="Naira Naouar <nanao@psb.ugent.be>",version="1.0.0",unlink=T,verbose=T) > makePDpackage("At35b_MR_v04-2_TIGRv5.bpmap",file1="At35b_MR_v04.cif", manufacturer="affymetrix", type="tiling",extra=extra) affymetrix tiling The package will be called tilingcdf Array identified as having 2560 rows and 2560 columns. Creating package in /group/biocomp/cbd/users/nanao/TilingData/LIB/BPMAP/tilingcdf [1] "tilingcdf" ******* End of R code ************** *** On Unix **** Then I checked and built the packages with R CMD check tilingcdf and R CMD build tilingcdf *** End of Unix *** Then I reproduced exactly the same error as below. Naira Benilton Carvalho wrote: > they were supposed to match 1:1.... > > b > > On Dec 3, 2007, at 5:14 AM, Naira Naouar wrote: > >> Hi Benilton, >> >> Sorry to annoy you but I have a new question concerning the oligo >> package. >> >> I would like to know how to access the MM value linked to a specific >> PM value. I know the position of the PM, and I would like to know >> what is the index of the MM value associated. >> >> >> Thx a lot, >> Naira >> >> -- >> ================================================================== >> Naira Naouar >> Tel:+32 (0)9 331 38 63 VIB Department of Plant >> Systems Biology, Ghent University >> Technologiepark 927, 9052 Gent, BELGIUM >> nanao@psb.ugent.be http://www.psb.ugent.be >> ================================================================== >> >> >> *From: *Naira Naouar <nanao@psb.ugent.be <mailto:nanao@psb.ugent.be>> >> *Date: *November 30, 2007 5:39:01 AM EST >> *To: *Bioconductor@stat.math.ethz.ch >> <mailto:Bioconductor@stat.math.ethz.ch> >> *Subject: **[BioC] Oligo package and tiling arrays - PM and MM* >> >> >> Dear all, >> >> I am using the oligo package to analyse affymetrix tiling array data and >> I don't understand why PM and MM do not have the same length... >> Here is the code: >> >>> #### READ CEL FILES >> >>> TOTAL_DATA = read.celfiles(exp_file,pk="tilingcdf") >> Incompatible phenoData object. Created a new one. >> Platform design info loaded. >> >>> x=pmindex(TOTAL_DATA) >>> length(x) >> [1] 3092374 >>> y=mmindex(TOTAL_DATA) >>> length(y) >> [1] 3092338 >> >>> sessionInfo() >> R version 2.5.0 (2007-04-23) >> x86_64-unknown-linux-gnu >> >> locale: >> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C >> >> attached base packages: >> [1] "splines" "tools" "stats" "graphics" "grDevices" >> "utils" >> [7] "datasets" "methods" "base" >> >> other attached packages: >> tilingcdf oligo BufferedMatrixMethods >> "1.0.0" "1.0.2-6" "1.0.0" >> BufferedMatrix RSQLite DBI >> "1.0.1" "0.5-6" "0.2-3" >> affyio Biobase >> "1.4.1" "1.14.0" >> >> Thanks, >> Naira >> >> -- >> ================================================================== >> Naira Naouar >> >> Tel:+32 (0)9 331 38 63 >> VIB Department of Plant Systems Biology, Ghent University >> Technologiepark 927, 9052 Gent, BELGIUM >> nanao@psb.ugent.be http://www.psb.ugent.be >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch <mailto:Bioconductor@stat.math.ethz.ch> >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> > -- ================================================================== Naira Naouar Tel:+32 (0)9 331 38 63 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao@psb.ugent.be http://www.psb.ugent.be ================================================================== ]