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
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> 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
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