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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 14:10:17 -0700
 

...and by the way, what is your sessionInfo(), i.e. what does the
following report?

> library("aroma.affymetrix");
> sessionInfo();

/Henrik

On Thu, Apr 5, 2012 at 1:55 PM, Henrik Bengtsson
<henrik.bengtsson@aroma-project.org> wrote:
> 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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