search for: cdfname

...* the dots list ("...") containing a list a parameters to pass to CDF function; and calls several goodness-of-fit tests on the given data values against the given distribution. That is: ##### BEGIN CODE SNIP ##### # Covert a distribution name to the related CDF function name distname2cdfname <- function( dist ) { if ( dist == "beta" ) { return( "pbeta" ); } if ( dist == "cauchy" ) { return( "pcauchy" ); } # many other and personalized (e.g. pareto, ...) distributions ... return( "" ); # fall-back case } # Performs some...

...nstalled this properly but I still get the same error: Could not find array definition file ' hu6800cdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. I've tried specifying the cdfname file by using data<-ReadAffy(cdfname="hu6800cdf") but it still returns the same error. The version of R that I'm using is 2.15 and the bioconductor version is 2.10. Does anyone know how to solve this? Thanks, srod -- View this message in context: http://r.789695.n4.nabble.c...

...types Affymettrix HGU133A_2 and HGU133_Plus_2. I have my files to be read in in one directory together with a white space delimited file describing them (covdesc). In this directory I give a command: > merge <- read.affy.mixed() Error in merged[[i]] : subscript out of bounds Error in cdfName(merged[[i]]) : error in evaluating the argument 'object' in selecting a method for function 'cdfName' > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats...

...ilenames, phenoData = l$phenoData, description = l$description, notes = notes, compress = compress, rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, verbose = verbose, normalize = normalize, background = background, bgversion = bgversion, destructive = destructive, cdfname = cdfname) 3: justRMA() aborting ... /var/spool/sge/tachyon1145/job_scripts/477103: line 21: 22829 Segmentation fault /home01/e133ywc/R/R-2.13.0/bin/Rscript /scratch/e133ywc/big/198/198.R -- View this message in context: http://r.789695.n4.nabble.com/cause-memory-not-mapped-tp3593833p3593833...

Hi all , I have one query. i have list of some .cel files. in my program i have to mention the path of these .cel files part of my program is, rna.data<-exprs(justRMA(filenames=file.names, celfile.path=*datadir*, sampleNames=sample.names, phenoData=pheno.data, cdfname=cleancdfname(hg18_Affymetrix U133A))) in the place of "datadir" i have to mention the character string of the directory of these .cel files. I don't know how to give the path for all these files. i set the path as given below, > rna.data<-exprs(justRMA(filenames=file.names,...

...l, I am meeting some problems with memory allocation. I know it is an old issue, I'm sorry. I looked for a solution in the FAQs and manuals, mails, but without finding the working answer. I really hope you can help me. For instance, if I try to read micorarray data I get: > mab=ReadAffy(cdfname="hgu133plus2cdf") Error: cannot allocate vector of size 858.0 Mb > I get similar errors with smaller objects, smaller data sets or other procedures ("Error: cannot allocate vector of size 123.0 Mb"). I'm running R with Suse 11.1 Linux OS, on two Xeon processors (8 core...

I'm working on Human Exon Array 1.0 ST. I'm getting normalized data fine but I'm running into problems with QC. QCReport gives me the following error: > load(file= "huex10stv2cdf.rda") > exon.data at cdfName <- "huex10stv2cdf" > QCReport(exon.data, file = "QCReport.pdf") Error in as.vector(ans[[i]][, i.probes]) : subscript out of bounds Your insight is very much appreciated!! Dorothy

...e? tried reading as text, gzipped text, binary, gzipped binary, command console and gzipped command console formats Also, I tried the command read.celfile in package "affyio" and it works, > x<-read.celfile("CH1.CEL") > str(x) List of 6 $ HEADER :List of 9 ..$ cdfName : chr "Axiom_GW_ASI_SNP" ..$ CEL dimensions : int [1:2] 1190 1190 ..$ GridCornerUL : int [1:2] 0 0 ..$ GridCornerUR : int [1:2] 1189 0 ..$ GridCornerLR : int [1:2] 1189 1189 ..$ GridCornerLL : int [1:2] 0 1189 ..$ DatHeader : chr...

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Hi all, I'm just tried to start analysing some micro-array chips. And R was asking for this package. When I tried to install it it says that: Using R version 2.10.1, biocinstall version 2.5.10. Installing Bioconductor version 2.5 packages: [1] "hugene10stv1cdf" Please wait... Warning message: In getDependencies(pkgs, dependencies, available, lib) : package ?hugene10stv1cdf? is