What does the following output: library("R.filesets"); path <- Arguments$getReadablePath("rawData/C11/GenomeWideSNP_6/"); ds <- GenericDataFileSet$byPath(path); print(ds); print(lapply(ds, getFileSize));
/Henrik On Fri, Feb 10, 2012 at 9:40 AM, Angelina Chattopadhyay Mukherjee <angelina...@cancer.org.uk> wrote: > Hi, > > Apologies for the delay in responding to your message. I'm afraid I am still > struggling with the error. My subdirectory 'GenomeWideSNP_6' does contain > .CEL files and I get the same error message. I'm sorry to trouble you again > but could you please advise what I should do? > > Kind regards, > Angelina > > > ________________________________________ > From: aroma-affymetrix@googlegroups.com [aroma-affymetrix@googlegroups.com] > On Behalf Of Henrik Bengtsson [henrik.bengts...@aroma-project.org] > Sent: 02 February 2012 05:05 > To: aroma-affymetrix@googlegroups.com > Subject: Re: [aroma.affymetrix] doCRMAv2 error > > Hi, > > first, I apologies that you had problems post your message; I just > noticed that there were several messages "on hold" to be approved by > the moderators. Normally we get a notice about this, but for some > reason we didn't get it. Now to your question... > > On Fri, Jan 27, 2012 at 12:17 AM, Angelina Chattopadhyay Mukherjee > <angelina...@cancer.org.uk> wrote: >> Hi, >> >> I checked my annotation files and found I'm using the ones shown on the >> aroma website: GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl , >> GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp, >> GenomeWideSNP_6,HB20080710.acs, GenomeWideSNP_6,Full.cdf. >> >> I'm using the correct directory structure as well. > > Even if I don't see it, I assume that the annotationData/ structure is > correct, because otherwise you wouldn't have been able to setup the > 'cdf' AffymetrixCdfFile object below. > >> I'd be grateful if anyone could help me with this error message: >> >> >>> dsList <- doCRMAv2(dataSet, cdf=cdf, combineAlleles=FALSE, verbose=verbose); >> 20120119 17:40:06|CRMAv2... >> 20120119 17:40:06| CRMAv2/Setting up CEL set... >> Error in list(`doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose >> = verbose)` = <environment>, : >> >> [2012-01-19 17:40:06] Exception: Cannot create AffymetrixCelSet. No such >> directory: C11/GenomeWideSNP_6 > > This basically says that it cannot find directory > > rawData/C11/GenomeWideSNP_6/ > > which should contain *.CEL files. Note that regardless of the CDF, > the subdirectory should be "GenomeWideSNP_6/" (not > "GenomeWideSNP_6,Full/"). > > Hope this helps > > /Henrik > >> at throw(Exception(...)) >> at throw.default("Cannot create ", class(static)[1], ". No such directory: >> ", >> at throw("Cannot create ", class(static)[1], ". No such directory: ", path) >> at method(static, ...) >> at AffymetrixCelSet$byName(dataSet, ..., verbose = less(verbose, 50), >> .onUnkno >> at doCRMAv2.character(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = >> ve >> at doCRMAv2(dataSet, cdf = cdf, combineAlleles = FALSE, verbose = verbose) >> >> >> >> My session info is: >> >>> sessionInfo() >> R version 2.14.1 (2011-12-22) >> Platform: x86_64-pc-linux-gnu (64-bit) >> >> locale: >> [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 >> [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 >> [7] LC_PAPER=C LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] sfit_0.2.0 aroma.affymetrix_2.4.1 affxparser_1.26.2 >> [4] aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.4.3 >> [7] aroma.light_1.22.0 matrixStats_0.4.3 R.rsp_0.7.1 >> [10] R.cache_0.5.2 R.filesets_1.1.4 digest_0.5.1 >> [13] R.utils_1.9.11 R.oo_1.8.3 R.methodsS3_1.2.1 >> >> >> NOTICE AND DISCLAIMER >> This e-mail (including any attachments) is intended for the above-named >> person(s). 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