Dear Benilton, Thank you for your reply. I tried crlmm package for normalizing and estimating copy number for Affy SNP6.0 data. The data includes 74 CEL files, it is a prostate cancer dataset downloaded from GEO sessioin id GSE14996. I ran crlmm, cnrma, snprma successfully, however,I failed at running computeCopynumber, which gave me NA for all the results. I attached the code, some output and sessionInfo() below. I read crlmm vignettes for copy number, genotyping and downstream analysis from the following webpage: http://bioconductor.org/packages/2.4/bioc/html/crlmm.html, however I still couldn't figure out the problem. It would be greatly appreciated if you could give me some hints. Thank you very much, Ashley ##################### R code, some output and sessionInfo ############################# R> library(crlmm) R> library(genomewidesnp6Crlmm) R> celFiles <- list.celfiles() R> outdir <- "/scratch/AshleyL/CEL_FILE" R> gender <- rep(1,74) # 1 is male, 2 is female R> if (!exists("crlmmResult")) { if (file.exists(file.path(outdir, "crlmmResult.rda"))) { load(file.path(outdir, "intensities.rda")) load(file.path(outdir, "crlmmResult.rda")) } else { crlmmResult <- crlmm(celFiles, gender=gender, save.it = TRUE, intensityFile = file.path(outdir, "intensities.rda")) save(crlmmResult, file = file.path(outdir, "crlmmResult.rda")) } } R> # Quantile normalize the nonpolymorphic probes and save the results. R> if (!exists("cnrmaResult")) { if (file.exists(file.path(outdir, "cnrmaResult.rda"))) load(file.path(outdir, "cnrmaResult.rda")) else { cnrmaResult <- cnrma(celFiles, cdfName = "genomewidesnp6") save(cnrmaResult, file = file.path(outdir, "cnrmaResult.rda")) } } R> # Do snprma for quantile normalization and summarization of polymorphic probes and save the results. R> if (!exists("snprmaOutput")) { if (file.exists(file.path(outdir, "snprmaOutput.rda"))) load(file.path(outdir, "snprmaOutput.rda")) else { snprmaOutput <- snprma(celFiles) save(snprmaOutput, file=file.path(outdir,"snprmaOutput.rda")) } } R> # Estimate copy number R> A<- snprmaOutput[["A"]] R> B<- snprmaOutput[["B"]] R> genotypes <- crlmm:::calls(crlmmResult) R> conf <- confs(crlmmResult) R> gender <- crlmmResult$gender R> SNR <- crlmmResult$SNR R> NP <- cnrmaResult$NP R> dts <- celDates(celFiles) R> table(format(dts, "%d %b %Y")) R> SNRmin <- 5 R> require(Biobase) R> sns <- sampleNames(crlmmResult) R> plate <- substr(basename(sns), 74, 74) R> plate <- basename(sns) R> table(plate) R> table(format(dts, "%d %b %Y"), plate) R> if (!exists("env")) { if (!file.exists(file.path(outdir, paste("env_chr", CHR, ".rda", sep = "")))) { env <- new.env() CHR <- 23 computeCopynumber(chrom = CHR, A = A, B = B, calls = genotypes, conf = conf, NP = NP, plate = plate, envir = env, DF.PRIOR = 50, MIN.OBS = 1, SNR = SNR,bias.adj=TRUE, gender=gender, SNRmin = SNRmin) save(env, file = file.path(outdir, paste("env_chr", CHR, ".rda", sep = ""))) } else { load(file.path(outdir, paste("env_chr", CHR, ".rda", sep = ""))) } } R> require(oligoClasses) R> path <- system.file("extdata", package = "genomewidesnp6Crlmm") R> load(file.path(path, "snpProbes.rda")) R> load(file.path(path, "cnProbes.rda")) R> position <- snpProbes[match(env[["snps"]], rownames(snpProbes)), "position"] R> position.np <- cnProbes[match(rownames(env[["NP"]]), rownames(cnProbes)), "position"] R> CA <- env[["CA"]] R> CB <- env[["CB"]] R> snpCT <- CA + CB R> npCT <- env[["CT"]] R> CT <- rbind(snpCT, npCT) R> dimnames(CT) <- list(c(env[["snps"]], rownames(env[["NP"]])), env[["sns"]]) R> dim(A) [1] 906600 74 R> dim(B) [1] 906600 74 R> dim(NP) [1] 937223 74 R> dim(CT) [1] 86086 74 R> A[1:5,1:5] [,1] [,2] [,3] [,4] [,5] [1,] 2810 2564 2588 3271 3346 [2,] 225 228 238 244 595 [3,] 1135 935 1055 821 1096 [4,] 504 486 1558 512 606 [5,] 1574 1756 1978 1797 1653 R> B[1:5,1:5] [,1] [,2] [,3] [,4] [,5] [1,] 2424 2088 2484 3433 2991 [2,] 624 720 802 844 617 [3,] 4173 3479 3217 3221 3235 [4,] 2179 1904 1380 1786 1686 [5,] 344 391 420 409 333 R> NP[1:5,1:5] GSM374529.CEL GSM374530.CEL GSM374531.CEL GSM374532.CEL GSM374533.CEL CN_473963 1926 1769 1001 903 1253 CN_473964 5502 5657 4295 3041 4961 CN_473965 4274 3457 2812 1822 3042 CN_477984 4175 3931 3538 2780 2280 CN_473981 1606 1571 1091 624 985 R> CT[1:5,1:5] GSM374529.CEL GSM374530.CEL GSM374531.CEL GSM374532.CEL SNP_A-1998091 NA NA NA NA SNP_A-1998092 NA NA NA NA SNP_A-1998095 NA NA NA NA SNP_A-1998097 NA NA NA NA SNP_A-1998099 NA NA NA NA GSM374533.CEL SNP_A-1998091 NA SNP_A-1998092 NA SNP_A-1998095 NA SNP_A-1998097 NA SNP_A-1998099 NA # Somehow, results from computeCopynumber are all NA. R> sessionInfo() R version 2.8.1 (2008-12-22) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=C attached base packages: [1] tools stats graphics grDevices utils datasets methods [8] base other attached packages: [1] oligoClasses_1.4.0 Biobase_2.2.2 [3] genomewidesnp6Crlmm_1.0.2 crlmm_1.2.4 loaded via a namespace (and not attached): [1] affyio_1.8.1 annotate_1.18.0 AnnotationDbi_1.4.3 [4] DBI_0.2-4 genefilter_1.20.0 mvtnorm_0.9-4 [7] preprocessCore_1.2.1 RSQLite_0.7-0 splines_2.8.1 [10] survival_2.34-1 > On Fri, Aug 21, 2009 at 11:46 AM, Benilton Carvalho <bcarvalh@jhsph.edu>wrote: > Dear Ashley, > > you didn't provide your sessionInfo(). It's been a while we don't use > BufferedMatrix in oligo, so I'm guessing you need to update oligo. > > For genotyping SNP 6.0 chips, this is not the recommended workflow. > > A) Using oligo, you should follow the vignette: > > > http://www.bioconductor.org/packages/2.4/bioc/vignettes/oligo/inst/d oc/oligo.pdf > > ie, pretty much: > > library(oligo) > filenames <- list.celfiles() > outputDir <- "someDirThatOligoWillCreateForYou" > crlmm(filenames, outputDir) > > B) We have developed an enhanced version of oligo, implemented in the > 'crlmm' package, in which case you're asked to follow: > > > http://www.bioconductor.org/packages/2.4/bioc/vignettes/crlmm/inst/d oc/genotyping.pdf > > HTH, > > b > > > On Aug 21, 2009, at 1:15 PM, Ashley Lin wrote: > > Dear all, >> >> I am trying to use oligo to analyze 75 Affy SNP6.0 chips. I have installed >> BufferedMatrix, but when I do: >> >> library(oligo) >>> filenames<-dir(pattern="CEL$") >>> rawData <- read.celfiles(filenames) >>> preProcessedData <- snprma(rawData) >>> >> >> It gave me an error message "Error in function (classes, fdef, mtable) : >> unable to find an inherited method for function "subBufferedMatrix", for >> signature "matrix". >> >> What could be wrong? >> >> Thanks, >> Ashley Lin >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > [[alternative HTML version deleted]]