It works perfectly ! thanks morten > > if you want the matrix with the genotype calls: > > calls(crlmm_NSP) > > if you want the matrix with the confidence associated to each call: > > callsConfidence(crlmm_NSP) > > does that help? > > b > > On Mar 8, 2007, at 4:30 PM, morten mattingsdal wrote: > >> Hi again, >> >> Nice ! Now crlmm finishes with no errors and I can hardly wait to >> do linkage analysis on the results. But I'm afraid I have one final >> question for you. >> How to export the data to a txt file? Im used to work with exprSet >> objects, and I took a shot at converting the results from crlmm >> using the code (with works for ordinary rma, gcrma and expresso >> "returns"): >> >>> out_NSP=as.matrix(exprs(crlmm_NSP)) >>> Error in function (classes, fdef, mtable) : >>> unable to find an inherited method for function "exprs", >>> for signature "SnpCallSet" >>> Error in as.matrix(exprs(crlmm_NSP)) : error in evaluating the >>> argument 'x' in selecting a method for function 'as.matrix' >> >> Ideally I want a matrix with columns corresponding to arrays and >> rows corresponding to individual probe ID. >> >> Is this possible ? >> >> best >> morten >> >> >> >>> Hi Morten, >>> >>> I'm writing a vignette to help users with oligo. My bad! Sorry for >>> that. >>> >>> All you need to do is give a file name... if the file does not exist, >>> it'll be created... if it exists, it'll be loaded. >>> >>> For example, try the following: >>> >>> crlmm_NSP=crlmm(rma_NSP, correctionFile="nspCorrection.rda") >>> >>> The reason this is required (at least for now) is because the EM >>> algorithm may take a long time depending on the sample size. So, once >>> it is done, it saves the results in this correctionFile... which you >>> can just load later in case you want to run CRLMM again. >>> >>> If for some reason you need to run CRLMM on the exact same data >>> (rma_NSP), by using >>> >>> crlmm_NSP=crlmm(rma_NSP, correctionFile="nspCorrection.rda") >>> >>> the EM step will be skipped and loaded from nspCorrection.rda >>> instead. >>> >>> b >>> >>> On Mar 7, 2007, at 9:55 AM, Morten Mattingsdal wrote: >>> >>>> Hi Benilton, >>>> >>>> Readning the data, loading annotation libraries and rma >>>> normalizting goes perfect! >>>> But I encounter an error in crlmm, which will probably expose my >>>> ignorance here, but crlmm complains about a "correctionFile is not >>>> found". >>>> >>>>> crlmm_NSP=crlmm(rma_NSP) >>>>> Error in crlmm(rma_NSP) : Provide correctionFile. >>>>> If the correctionFile is not found, it will be created and it will >>>> contain the EM results. >>>> >>>> The error claims, if not found it will be created. I don't think it >>>> is created, although I have an R object called "reference" >>>> >>>> The crlmm doc says: The 'correction' argument is a list with the >>>> following elements: >>>> 'f0' (scalar), 'fs' (numeric vector), 'pis' (numeric matrix) and >>>> 'snr'. >>>> >>>> I cant seem to figure out the nature of these correction elements >>>> nor the data format of this file. >>>> Could you be so kind and explain a bit what this means ? >>>> >>>> regards >>>> morten >>>> >>>> >>>> NB Ill just paste all commands and output for your leisure >>>> >>>>> library(oligo) >>>> >>>>> files <- list.celfiles() >>>> >>>>> files() >>>> [1] "1580_Nsp1_090207.CEL" "1620_Nsp1_020307.CEL" >>>> "1736_Nsp1_020307.CEL" >>>> [4] "1812_Nsp1_020307.CEL" "355_Nsp1_090207.CEL" >>>> "4379_Nsp1_020307.CEL" >>>> [7] "4436_Nsp1_020307.CEL" "5968_Nsp1_020307.CEL" >>>> "635_Nsp1_090207.CEL" >>>> [10] "654_Nsp1_090207.CEL" "659_Nsp1_090207.CEL" >>>> "680_Nsp1_090207.CEL" >>>> >>>>> NSP <- read.celfiles(files) >>>> Incompatible phenoData object. Created a new one. >>>> >>>> >>>> Welcome to the pd.Mapping250K_Nsp prototype pdInfo package >>>> WARNING: DO NOT USE THIS PACKAGE FOR ANY ANALYSIS. >>>> THIS PACKAGE IS FOR INTERFACE PROTOTYPE USE ONLY! >>>> THE DATA HAS NOT BEEN VALIDATED AND LIKELY HAS ERRORS. >>>> Have fun! >>>> >>>> Platform design info loaded. >>>> >>>>> rma_NSP <- snprma(NSP) >>>> Position -4 >>>> Position -2 >>>> Position -1 >>>> Position 0 >>>> Position 1 >>>> Position 3 >>>> Position 4 >>>> Loading required package: pd.mapping250k.nsp.crlmm.regions >>>> Calculating Expression >>>> >>>>> crlmm_NSP=crlmm(rma_NSP) >>>> Error in crlmm(rma_NSP) : Provide correctionFile. >>>> If the correctionFile is not found, it will be created and it will >>>> contain the EM results. >>>> >>>> >>>>> sessionInfo() >>>> R version 2.5.0 Under development (unstable) (2007-03-04 r40813) >>>> x86_64-unknown-linux-gnu >>>> >>>> locale: >>>> LC_CTYPE=no_NO;LC_NUMERIC=C;LC_TIME=C;LC_COLLATE=C;LC_MONETARY=C;LC_ >>>> ME >>>> SSAGES=C;LC_PAPER=C;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASURE >>>> ME >>>> NT=C;LC_IDENTIFICATION=C >>>> >>>> attached base packages: >>>> [1] "splines" "tools" "stats" "graphics" "grDevices" >>>> "utils" [7] "datasets" "methods" "base" >>>> other attached packages: >>>> pd.mapping250k.nsp.crlmm.regions pd.mapping250k.nsp >>>> "0.1.0" "0.1.5" >>>> geneplotter lattice >>>> "1.13.7" "0.14-16" >>>> annotate oligo >>>> "1.13.6" "0.99.82" >>>> BufferedMatrixMethods BufferedMatrix >>>> "0.1.1" "0.1.27" >>>> RSQLite DBI >>>> "0.4-20" "0.1-12" >>>> affyio Biobase >>>> "1.3.3" "1.13.39" >>>> >>>> Benilton Carvalho wrote: >>>>> Hi Morten, >>>>> >>>>> the 'safe' versions will become available with BioC 2.0. >>>>> >>>>> My question, regarding the email you send next (about using >>>>> makePlatformDesign for SNP arrays), that's not required anymore. >>>>> All you need is in that oligoAddOns.tar.gz. All you need to do is >>>>> install the packages and use the latest oligo. >>>>> >>>>> Let me know how things go, >>>>> >>>>> b >>>>> >>>>> On Mar 7, 2007, at 5:45 AM, Morten Mattingsdal wrote: >>>>> >>>>>> Hello everyone, >>>>>> >>>>>> Ive managed to get the oligo package and the crlmm function up and >>>>>> running. Ive also installed the meta-data libraries from this URL >>>>>> http://www.biostat.jhsph.edu/~bcarvalh/oligoAddOns.tar.gz >>>>>> provided by Benliton >>>>>> >>>>>> but when I run the commands: >>>>>> >>>>>>> files <- list.celfiles() >>>>>>> snpFSet <- read.celfiles(files) >>>>>>> >>>>>>> Welcome to the pd.Mapping250K_Nsp prototype pdInfo package >>>>>>> WARNING: DO NOT USE THIS PACKAGE FOR ANY ANALYSIS. >>>>>>> THIS PACKAGE IS FOR INTERFACE PROTOTYPE USE ONLY! >>>>>>> THE DATA HAS NOT BEEN VALIDATED AND LIKELY HAS ERRORS. >>>>>>> Have fun! >>>>>> >>>>>> Im am happy that this information is warning me, but to my point: >>>>>> - When will the "safe" mapping libraries come? >>>>>> - Can I build this by myself ? >>>>>> >>>>>> I want to compare brlmm from Affymetrix and crlmm from BioC >>>>>> genotype >>>>>> calls for my data >>>>>> >>>>>> regards >>>>>> morten >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>> >>>>> >>>>> . >>>>> >> >> ____________________________________________________________ >> FREE ONLINE PHOTOSHARING - Share your photos online with your >> friends and family! >> Visit http://www.inbox.com/photosharing to find out more!