As a follow up, my guess is that you're using download.file() in R to
download the file, correct? If so, you *have to* to set argument
mode="wb". Better/much safer, use:
library("R.utils");
downloadFile("http://bcgc.lbl.gov/cdfFiles/HuEx-1_0-st-v2,A20071112,EP/HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf";);
/Henrik
On Wed, Aug 29, 2012 at 11:52 AM, Henrik Bengtsson
<[email protected]> wrote:
> 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 <[email protected]> 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 <[email protected]>
>> 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
>> <[email protected]> wrote:
>>>
>>> Comments below...
>>>
>>> On Tue, Aug 28, 2012 at 4:06 AM, Maria Rodrigo <[email protected]> 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$byChipType(chipType,
>>> > + tags = "core,A20071112,EP")
>>> >> cdf2
>>> >
>>> > ## AffymetrixCdfFile:
>>> > ## Path: annotationData/chipTypes/HuEx-1_0-st-v2
>>> > ## Filename: HuEx-1_0-st-v2,core,A20071112,EP.cdf
>>> > ## Filesize: 38.25MB
>>> > ## Chip type: HuEx-1_0-st-v2,core,A20071112,EP
>>> >
>>> > ## RAM: 0.00MB
>>> > ## File format: v4 (binary; XDA)
>>> > ## Dimension: 2560x2560
>>> > ## Number of cells: 6553600
>>> > ## Number of units: 18708
>>> > ## Cells per unit: 350.31
>>> > ## Number of QC units: 1
>>> >
>>> > On 27 August 2012 02:09, Henrik Bengtsson
>>> > <[email protected]> wrote:
>>> >>
>>> >> Hi,
>>> >>
>>> >> I see nothing wrong with your script. I suspect that the CDF you've
>>> >> downloaded got corrupted or something. Do you get the same output as
>>> >> below:
>>> >>
>>> >> > library("aroma.affymetrix")
>>> >> > cdf <- AffymetrixCdfFile$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
>>> >> <[email protected]> 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
>>> >> > [email protected]
>>> >> > 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 [email protected]
>>> >> 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 [email protected]
>>> > 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 [email protected]
>>> 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 [email protected]
>> 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 [email protected]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
