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

[Henrik Bengtsson]

Hi.

On Wed, Apr 4, 2012 at 7:57 AM, Fred Foucault
<frederic...@gmail.com> 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.
>
>
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[Frederic 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

[Pierre Neuvial]

Hi,

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

[Frederic 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 :

[Henrik Bengtsson]

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

[Henrik Bengtsson]

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

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

/Henrik

[Frederic 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 

[ck...@ebi.ac.uk]

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