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To:aroma-affymetrix@googlegroups.com From:Henrik Bengtsson Subject:Re: [aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed Date:Thu, 5 Apr 2012 13:55:54 -0700
 

Hi,

first of all, there is a very simple reason for this, we just have to
find out why. My best guess now is that one of the files are
incomplete. Start a fresh R session and verify that you get the
exactly same *file sizes* as below:

> library("aroma.affymetrix");
> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full");
> ds <- GenericDataFileSet$byPath(getPath(cdf));
> print(as.list(ds));

[[1]]
GenericDataFile:
Name: GenomeWideSNP_6
Tags: Full,na31,hg19,HB20110328
Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl
File size: 7.18 MB (7526452 bytes)
RAM: 0.00 MB

[[2]]
GenericDataFile:
Name: GenomeWideSNP_6
Tags: Full,na31,hg19,HB20110328
Full name: GenomeWideSNP_6,Full,na31,hg19,HB20110328
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp
File size: 8.97 MB (9407867 bytes)
RAM: 0.00 MB

[[3]]
GenericDataFile:
Name: GenomeWideSNP_6
Tags: Full
Full name: GenomeWideSNP_6,Full
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full.CDF
File size: 470.44 MB (493291745 bytes)
RAM: 0.00 MB

[[4]]
GenericDataFile:
Name: GenomeWideSNP_6
Tags: HB20080710
Full name: GenomeWideSNP_6,HB20080710
Pathname: annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs
File size: 170.92 MB (179217531 bytes)
RAM: 0.00 MB

/Henrik

On Thu, Apr 5, 2012 at 5:40 AM, Frederic Foucault
<frederic.foucault@gmail.com> wrote:
> Hi,
>
> Here is the path
>>path <- getPath(cdf)
>> list.files(path)
> [1] "GenomeWideSNP_6,Full,HB20080710.acs"
> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl"
> [3] "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"
> "GenomeWideSNP_6,Full.cdf"
>
> Frederic
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a crit:
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> Im following the vignette for ACNE.
>> I installed the annotation data in \test\annotationData\chipTypes
>> \GenomeWideSNP6.0
>>
>> "GenomeWideSNP_6,Full,HB20080710.acs"
>> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ufl"
>> "GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"
>> "GenomeWideSNP_6,Full.cdf"
>>
>> GenomeWideSNP_6,Full.cdf is from Affymetrix while the three others are
>> from aroma
>>
>> here is the error :
>> gi <- getGenomeInformation(cdf);
>> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
>> [2012-04-04 16:48:48] Exception: Failed to retrieve genome information
>> for this chip type: GenomeWideSNP_6
>>
>> at #02. getGenomeInformation.AffymetrixCdfFile(cdf)
>> - getGenomeInformation.AffymetrixCdfFile() is in environment
>> 'aroma.affymetrix'
>>
>> at #01. getGenomeInformation(cdf)
>> - getGenomeInformation() is in environment
>> 'aroma.affymetrix'
>>
>>
>> Thank you for your help
>> Frederic
>>
> --
> 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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--
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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