Ok, there is something wrong with your downloads. Downloading that URL should give you a file that is exactly 40,108,891 bytes. Your downloaded file is of a different size. I don't know how you're downloading and with what software, but I recommend that you try using a different software, a different computer, and as an extreme backup from a different internet connection (work vs home)?
/Henrik On Wed, Aug 29, 2012 at 9:01 AM, Maria Rodrigo <mrod...@gmail.com> wrote: > Hi Henrik, > > Sorry, I also checked the file size and checksum and I forgot to add them to > the email; they do not match your results, see below: > > >> 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 >> getFileSize(cdf) > [1] 40119256 >> getChecksum(cdf) > [1] "4edf1818f913069ba314e1358fc232a5" >> packageDescription("affxparser") > Package: affxparser > Version: 1.28.1 > Date: 2012-03-30 > Title: Affymetrix File Parsing SDK > Author: Henrik Bengtsson, James Bullard, Robert Gentleman, Kasper > Daniel Hansen, Martin Morgan > Maintainer: Kasper Daniel Hansen <khan...@jhsph.edu> > Description: Package for parsing Affymetrix files (CDF, CEL, CHP, > BPMAP, BAR). It provides methods for fast and memory efficient > parsing of Affymetrix files using the Affymetrix' Fusion SDK. > Both ASCII- and binary-based files are supported. Currently, > there are methods for reading chip definition file (CDF) and a > cell intensity file (CEL). These files can be read either in > full or in part. For example, probe signals from a few > probesets can be extracted very quickly from a set of CEL files > into a convenient list structure. > FusionDetails: Fusion SDK v1.1.0 > License: LGPL (>= 2) > Depends: R (>= 2.6.0) > Suggests: R.utils (>= 1.9.11), AffymetrixDataTestFiles > LazyLoad: yes > biocViews: Infrastructure, DataImport > Packaged: 2012-06-27 05:14:14 UTC; biocbuild > Built: R 2.15.1; i386-pc-mingw32; 2012-06-27 10:04:17 UTC; windows > > -- File: C:/Programmer/R/R-2.15.1/library/affxparser/Meta/package.rds > > Thanks!! > > Maria > > > > On 28 August 2012 21:05, Henrik Bengtsson > <henrik.bengts...@aroma-project.org> wrote: >> >> Comments below... >> >> On Tue, Aug 28, 2012 at 4:06 AM, Maria Rodrigo <mrod...@gmail.com> wrote: >> > 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, >> > 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). >> >> Let's skip this approach and focus on the first one. >> >> > >> > 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 >> >> And what does: >> >> > getFileSize(cdf) >> > getChecksum(cdf) >> >> give? That's critical in order to confirm that your download is not >> corrupt. Also, what does the following give: >> >> > packageDescription("affxparser") >> >> /Henrik >> >> >> 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. >> > >> > >> > 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. > > > 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/