Hi Henrik, Thanks for your reply.
I have checked what you ask for and the information from my cdf file and yours does not match, see output of "> cdf" in the code below. I have downloaded the file again from: http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20071112,EP/HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf I also downloaded the zipped folder HuEx-1_0-st-v2,R3,A20071112,EP.zip<http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20071112,EP/HuEx-1_0-st-v2,R3,A20071112,EP.zip>, containing .CDF files for core, extended, full and more. Their names do not include R3, but just the date. I tried the file for core probesets contained in the zipped folder, and this one matches yours 100% (see output of "> cdf2" below). Do you think there might be something wrong with the .CDF file on the website, or do you think it gets corrupted when I download it? I have downloaded it from several places, many times, I must say. > cdf <- AffymetrixCdfFile$byChipType(chipType, + tags = "coreR3,A20071112,EP") > cdf ## AffymetrixCdfFile: ## Path: annotationData/chipTypes/HuEx-1_0-st-v2 ## Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf ## Filesize: 38.26MB ## Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP ## RAM: 0.00MB ## File format: v4 (binary; XDA) ## Dimension: 10x3328 ## Number of cells: 33280 ## Number of units: 1226050061 ## Cells per unit: 0.00 ## Number of QC units: 65536 > cdf2 <- AffymetrixCdfFile$byChipType(chipType, + tags = "core,A20071112,EP") > cdf2 ## AffymetrixCdfFile: ## Path: annotationData/chipTypes/HuEx-1_0-st-v2 ## Filename: HuEx-1_0-st-v2,core,A20071112,EP.cdf ## Filesize: 38.25MB ## Chip type: HuEx-1_0-st-v2,core,A20071112,EP ## RAM: 0.00MB ## File format: v4 (binary; XDA) ## Dimension: 2560x2560 ## Number of cells: 6553600 ## Number of units: 18708 ## Cells per unit: 350.31 ## Number of QC units: 1 On 27 August 2012 02:09, Henrik Bengtsson < henrik.bengts...@aroma-project.org> wrote: > Hi, > > I see nothing wrong with your script. I suspect that the CDF you've > downloaded got corrupted or something. Do you get the same output as > below: > > > library("aroma.affymetrix") > > cdf <- AffymetrixCdfFile$byChipType(chipType, tags = > "coreR3,A20071112,EP"); > > cdf > ## AffymetrixCdfFile: > ## Path: annotationData/chipTypes/HuEx-1_0-st-v2 > ## Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf > ## Filesize: 38.25MB > ## Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP > ## RAM: 0.00MB > ## File format: v4 (binary; XDA) > ## Dimension: 2560x2560 > ## Number of cells: 6553600 > ## Number of units: 18708 > ## Cells per unit: 350.31 > ## Number of QC units: 1 > > getFileSize(cdf) > [1] 40108891 > > getChecksum(cdf) > [1] "e7b0bacd27699534d125b16266d7cc09" > > /Henrik > > > On Wed, Aug 15, 2012 at 4:30 AM, Maria Rodrigo-Domingo > <mrod...@gmail.com> wrote: > > Dear aroma team, > > > > > > > > I am using aroma.affymetrix for the exon array and I am having trouble > using > > one of your custom .CDF files. It is the one for core transcripts: > > “HuEx-1_0-st-v2,coreR3,A20071112,EP.CDF”, listed in > > http://aroma-project.org/node/122, under R3. I get an error when > setting up > > the cel set with that .CDF file: there seems to be a mismatch between > the > > number of cells on the .CDF file and on the .CEL files (please, see > below). > > I report the output of sessionInfo() and traceback() after the code. > > > > > > > > I have tried several other of your custom .CDF files (R3: extended and > full, > > R2: core) and I do not get any errors. I am actually using one .CDF file > > called “HuEx-1_0-st-v2,core,A20071112,EP.CDF” that works just fine. The > > only difference in the name is the missing R3 and I only realized after > my > > supervisor tried to test my script. I downloaded it one year ago and I > > assumed it was yours, but I cannot remember where I got it from and > cannot > > trace it back. > > > > > > > > I have downloaded the core R3 .CDF file several times from > > > http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20071112,EP/HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf > , > > to make sure I have the right version. > > > > Do you think there might be something wrong about the available file? Any > > ideas on how to solve this problem? Thank you very much for your help. > > > > > > > > Best, > > > > Maria Rodrigo > > > > > > > >> ds <- "AffyColonCancer" > > > >> chipType <- "HuEx-1_0-st-v2" > > > >> cdf <- AffymetrixCdfFile$byChipType(chipType, tags = > >> "coreR3,A20071112,EP") > > > >> cs <- AffymetrixCelSet$byName(ds, cdf = cdf) > > > > Error in method(static, ...) : > > > > [2012-08-15 12:47:07] Exception: Failed to setup a data set for any of 1 > > data directories located. The following reasons were reported: (1) Cannot > > set CDF. The specified CDF structure > ('HuEx-1_0-st-v2,coreR3,A20071112,EP') > > is not compatible with the chip type ('HuEx-1_0-st-v2') of the CEL file. > The > > number of cells do not match: 33280 != 6553600 (while trying > > 'rawData/AffyColonCancer/HuEx-1_0-st-v2'). > > > > > > > > at #02. method(static, ...) > > > > - method() is in environment 'aroma.affymetrix' > > > > > > > > at #01. AffymetrixCelSet$byName(ds, cdf = cdf) > > > > - AffymetrixCelSet$byName() is local of the calling function > > > > > > > >> sessionInfo() > > > > > > > > R version 2.15.1 (2012-06-22) > > > > Platform: i386-pc-mingw32/i386 (32-bit) > > > > > > > > locale: > > > > [1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252 > > LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C > > > > [5] LC_TIME=Danish_Denmark.1252 > > > > > > > > attached base packages: > > > > [1] stats graphics grDevices utils datasets methods base > > > > > > > > other attached packages: > > > > [1] aroma.affymetrix_2.5.0 affxparser_1.28.1 aroma.apd_0.2.3 > > R.huge_0.4.1 aroma.core_2.5.0 aroma.light_1.24.0 > > > > [7] matrixStats_0.5.2 R.rsp_0.8.2 R.devices_2.1.1 > > R.filesets_1.1.5 digest_0.5.2 R.cache_0.6.2 > > > > [13] R.utils_1.12.1 R.oo_1.9.8 R.methodsS3_1.4.2 > > BiocInstaller_1.4.7 > > > > > > > > loaded via a namespace (and not attached): > > > > [1] tools_2.15.1 > > > > > > > >> traceback() > > > > 11: modStop(cond) > > > > 10: abort.condition(cond) > > > > 9: abort(cond) > > > > 8: abort.default(msg, call = call) > > > > 7: abort(msg, call = call) > > > > 6: throw.Exception(Exception(...)) > > > > 5: throw(Exception(...)) > > > > 4: throw.default(msg) > > > > 3: throw(msg) > > > > 2: method(static, ...) > > > > 1: AffymetrixCelSet$byName(ds, cdf = cdf) > > > > -- > > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest > > version of the package, 2) to report the output of sessionInfo() and > > traceback(), and 3) to post a complete code example. > > > > > > You received this message because you are subscribed to the Google Groups > > "aroma.affymetrix" group with website http://www.aroma-project.org/. > > To post to this group, send email to aroma-affymetrix@googlegroups.com > > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > > -- > When reporting problems on aroma.affymetrix, make sure 1) to run the > latest version of the package, 2) to report the output of sessionInfo() and > traceback(), and 3) to post a complete code example. > > > You received this message because you are subscribed to the Google Groups > "aroma.affymetrix" group with website http://www.aroma-project.org/. > To post to this group, send email to aroma-affymetrix@googlegroups.com > To unsubscribe and other options, go to > http://www.aroma-project.org/forum/ > -- When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example. 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