[aroma.affymetrix] ACNE getGenomeInformation(cdf) failed

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[aroma.affymetrix] ACNE getGenomeInformation(cdf) failed

Fred Foucault
Hello,

I want to get allele specific copy number from SNP6 CL files
I´m 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

--
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Re: [aroma.affymetrix] ACNE getGenomeInformation(cdf) failed

Henrik Bengtsson-3
Hi.

On Wed, Apr 4, 2012 at 7:57 AM, Fred Foucault
<[hidden email]> wrote:
> Hello,
>
> I want to get allele specific copy number from SNP6 CL files
> I´m following the vignette for ACNE.
> I installed the annotation data  in \test\annotationData\chipTypes
> \GenomeWideSNP6.0

The name of that subdirectory is not correct.  Make sure it is
*exactly* as shown in the vignette.  See also
http://aroma-project.org/setup/

What puzzles me though is how you manage to setup the
AffymetrixCdfFile object 'cdf' in the first place.  You must have done
something different than:

chipType <- "GenomeWideSNP_6";
cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
print(cdf);

because that should also give a similar error.

/Henrik

>
> "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.
>
>
> 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 [hidden email]
> 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.


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[aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed

Fred Foucault
In reply to this post by Fred Foucault
Hello,

I follow the setup of the vignette but failed again

setwd("c:/Users/foucault/Bioinformatic/acne/Test/")
> library("aroma.affymetrix");
> library("ACNE");
> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);

> dataSet <- "GSE14996,testSet";
> chipType <- "GenomeWideSNP_6";
> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
> print(cdf);
AffymetrixCdfFile:
Path: annotationData/chipTypes/GenomeWideSNP_6
Filename: GenomeWideSNP_6,Full.cdf
Filesize: 470.44MB
Chip type: GenomeWideSNP_6,Full
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2572x2680
Number of cells: 6892960
Number of units: 1881415
Cells per unit: 3.66
Number of QC units: 4
> gi <- getGenomeInformation(cdf);
Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
[2012-04-05 10:12:33] 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




Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
Hello,

I want to get allele specific copy number from SNP6 CL files
I´m 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


Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
Hello,

I want to get allele specific copy number from SNP6 CL files
I´m 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


Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
Hello,

I want to get allele specific copy number from SNP6 CL files
I´m 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


Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
Hello,

I want to get allele specific copy number from SNP6 CL files
I´m 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


Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
Hello,

I want to get allele specific copy number from SNP6 CL files
I´m 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


Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
Hello,

I want to get allele specific copy number from SNP6 CL files
I´m 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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Re: [aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed

Pierre Neuvial
Hi,



On Thu, Apr 5, 2012 at 10:17 AM, Frederic Foucault
<[hidden email]> wrote:

> Hello,
>
> I follow the setup of the vignette but failed again
>
> setwd("c:/Users/foucault/Bioinformatic/acne/Test/")
>> library("aroma.affymetrix");
>> library("ACNE");
>> verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
>>
>> dataSet <- "GSE14996,testSet";
>
>> chipType <- "GenomeWideSNP_6";
>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="Full");
>> print(cdf);
> AffymetrixCdfFile:
> Path: annotationData/chipTypes/GenomeWideSNP_6
> Filename: GenomeWideSNP_6,Full.cdf
> Filesize: 470.44MB
> Chip type: GenomeWideSNP_6,Full
> RAM: 0.00MB
> File format: v4 (binary; XDA)
> Dimension: 2572x2680
> Number of cells: 6892960
> Number of units: 1881415
> Cells per unit: 3.66
> Number of QC units: 4
>
>> gi <- getGenomeInformation(cdf);
> Error in getGenomeInformation.AffymetrixCdfFile(cdf) :
> [2012-04-05 10:12:33] 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
>
>

Did you place all the annotation files in the
annotationData/chipTypes/GenomeWideSNP_6 folder ?
It looks that this one is missing :

"GenomeWideSNP_6,Full,na31,hg19,HB20110328.ugp"

Do these file appear in the output of

path <- getPath(cdf)
list.files(path)

If not, then add them and retry.
If yes then I'm missing something.

Cheers,

Pierre

Pierre

>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m 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
>>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m 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
>>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m 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
>>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m 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
>>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m 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
>>
>
> Le mercredi 4 avril 2012 16:57:18 UTC+2, Frederic Foucault a écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m 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.
>
>
> 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 [hidden email]
> 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.


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[aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed

Fred Foucault
In reply to this post by Fred Foucault
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 écrit :
Hello,

I want to get allele specific copy number from SNP6 CL files
I´m 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

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Re: [aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed

Henrik Bengtsson-4
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
<[hidden email]> 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 écrit :
>>
>> Hello,
>>
>> I want to get allele specific copy number from SNP6 CL files
>> I´m 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.
>
>
> 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 [hidden email]
> 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.


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Re: [aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed

Henrik Bengtsson-4
...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
<[hidden email]> 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
> <[hidden email]> 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 écrit :
>>>
>>> Hello,
>>>
>>> I want to get allele specific copy number from SNP6 CL files
>>> I´m 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.
>>
>>
>> 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 [hidden email]
>> 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.


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[aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed

Fred Foucault
In reply to this post by Fred Foucault
 Hi Henrik, Hi Pierre,
Thanks a lot for your precious helps.

Henrik , you are right: two files were not ofthe correct size: "GenomeWIDE....ufl" and "GenomeWIDE....ugp". I downloaded them again from aroma.org
Now, i will do the complete run of ACNE test of the GSE14996 dataset. Other questions will come...

Here is my R session info

R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
 [1] ACNE_0.5.0             MASS_7.3-17            aroma.affymetrix_2.5.0
 [4] affxparser_1.26.4      aroma.apd_0.2.0        R.huge_0.3.0         
 [7] aroma.core_2.5.0       aroma.light_1.22.0     R.rsp_0.7.5          
[10] R.cache_0.6.1          R.filesets_1.1.5       digest_0.5.2         
[13] R.utils_1.12.1         matrixStats_0.4.4      R.oo_1.9.3           
[16] R.methodsS3_1.2.2 

--
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[aroma.affymetrix] Re: ACNE getGenomeInformation(cdf) failed

ckong
Hi Henrik,

   Very similar to the issue above, I have checked the file size, which is fine. However this is the error I still encounter, any thoughts? 

Thanks
ck

> list.files(path)
[1] "GenomeWideSNP_6,Full,na33,hg19,dbsnp137,HB20140118.ufl"
[2] "GenomeWideSNP_6,Full,na33,hg19,dbsnp137,HB20140118.ugp"
[3] "GenomeWideSNP_6,Full.cdf"                              
[4] "GenomeWideSNP_6,HB20080710.acs"    

> gi<-getGenomeInformation(cdf)
[2018-05-30 16:14:36] 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'

Error: Failed to retrieve genome information for this chip type: GenomeWideSNP_6

├── annotationData
│   └── chipTypes
│       └── GenomeWideSNP_6
│           ├── GenomeWideSNP_6,Full,na33,hg19,dbsnp137,HB20140118.ufl
│           ├── GenomeWideSNP_6,Full,na33,hg19,dbsnp137,HB20140118.ugp
│           ├── GenomeWideSNP_6,Full.cdf
│           └── GenomeWideSNP_6,HB20080710.acs


On Tuesday, 10 April 2012 09:19:31 UTC+1, Frederic Foucault wrote:
 Hi Henrik, Hi Pierre,
Thanks a lot for your precious helps.

Henrik , you are right: two files were not ofthe correct size: "GenomeWIDE....ufl" and "GenomeWIDE....ugp". I downloaded them again from <a href="http://aroma.org" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Faroma.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHVrIsYJiybhyvlNcsVa2YgoNWHJw&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Faroma.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHVrIsYJiybhyvlNcsVa2YgoNWHJw&#39;;return true;">aroma.org
Now, i will do the complete run of ACNE test of the GSE14996 dataset. Other questions will come...

Here is my R session info

R version 2.14.0 (2011-10-31)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
 [1] ACNE_0.5.0             MASS_7.3-17            aroma.affymetrix_2.5.0
 [4] affxparser_1.26.4      aroma.apd_0.2.0        R.huge_0.3.0         
 [7] aroma.core_2.5.0       aroma.light_1.22.0     R.rsp_0.7.5          
[10] R.cache_0.6.1          R.filesets_1.1.5       digest_0.5.2         
[13] R.utils_1.12.1         matrixStats_0.4.4      R.oo_1.9.3           
[16] R.methodsS3_1.2.2 

--
--
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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