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/
