[aroma.affymetrix] AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0

2011-05-05 Thread richland
Hi,list,


 Here is my basic set up under my current working directory:~/project/

rawData/M7/GenomeWideSNP_6/
23..CEL  SJO023-snp6.CEL  25-snp6.CEL,26-snp6.CEL ...

==
annotationData/chipTypes/GenomeWideSNP_6/

GenomeWideSNP_6,Full.cdf
GenomeWideSNP_6,Full,na30,hg18,HB20100215.ufl
GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp
GenomeWideSNP_6,HB20080710.acs

I don't need sample information so there is no samples/ directory
under annotationData

I'm using R/2.12.0,  aroma.affymetrix v2.1.0 (2011-04-08)

#
ibrary(aroma.affymetrix)
verbose - Arguments$getVerbose(-8)
timestampOn(verbose)

chipType - GenomeWideSNP_6

cdf- AffymetrixCdfFile$byChipType(chipType,tags=Full)

print(cdf) # ok

dataSetName-M7;
cs - AffymetrixCelSet$byName(dataSetName,
 cdf=cdf,  verbose=-10)
failed:

it found all  6 cell files, but keeps looking form saf file in /
nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/aroma.affymetrix/
annotationData/samples/HapMap270.saf




Trying path #1 of 1...
  Path: rawData/M7/GenomeWideSNP_6
  Defining AffymetrixCelSet from files...
   Defining an AffymetrixCelSet object from files...
Path: rawData/M7/GenomeWideSNP_6
Pattern: [.](c|C)(e|E)(l|L)$
File class: AffymetrixCelFile
Scanning directory for files...
 Found 6 files/directories.
 Found 6 files.
Scanning directory for files...done
Defining 6 files...
1, 2, 3, 4, 5, 6,
Defining 6 files...done
Allocating a new AffymetrixCelSet instance...
 Arguments:
 Number of files: 6
  list()
Allocating a new AffymetrixCelSet instance...done
Updating newly allocated AffymetrixCelSet...
 Updating AffymetrixCelSet...
  Scanning for and applying sample annotation files...
   Loading all SampleAnnotationSet:s...
Identify all directories containing SAF files...
 All SAF files located:
 [1] /nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/
aroma.affymetrix/annotationData/samples/HapMap270.saf

Path (to the first file): /nfs_exports/apps/64-bit/gnu-apps/R/
libraries/2.12.0/aroma.affymetrix/annotationData/samples
 Total file size: 0.03 MB
 RAM: 0.00MB
Scanning for and applying sample annotation files...done
   Updating AffymetrixCelSet...done
  Defining AffymetrixCelSet from files...done
  Data set could not be setup for this path, because:
  cannot open the connection
 Trying path #1 of 1...done
Error in list(`AffymetrixCelSet$byName(dataSetName, cdf = cdf, verbose
= -10)` = environment,  :

[2011-05-05 10:46:03] Exception: Failed to setup a data set for any of
1 data directories located.
  at throw(Exception(...))
  at throw.default(sprintf(Failed to setup a data set for any of %d
data direct
  at throw(sprintf(Failed to setup a data set for any of %d data
directories lo
  at method(static, ...)
  at AffymetrixCelSet$byName(dataSetName, cdf = cdf, verbose = -10)
Calls: Anonymous ... method - throw - throw.default - throw -
throw.Exception
Setting up AffymetrixCelSet by name...done
Execution halted

===
I also tried to make a samples/ directory under annotationData/ ans
made a file called M7.saf. it also failed.

[1] rawData/M7/GenomeWideSNP_6
 Trying path #1 of 1...
  Path: rawData/M7/GenomeWideSNP_6
  Defining AffymetrixCelSet from files...
   Defining an AffymetrixCelSet object from files...
Path: rawData/M7/GenomeWideSNP_6
Pattern: [.](c|C)(e|E)(l|L)$
File class: AffymetrixCelFile
Scanning directory for files...
 Found 6 files/directories.
 Found 6 files.
Scanning directory for files...done
Defining 6 files...
1, 2, 3, 4, 5, 6,
Defining 6 files...done
Allocating a new AffymetrixCelSet instance...
 Arguments:
 Number of files: 6
  list()
Allocating a new AffymetrixCelSet instance...done
Updating newly allocated AffymetrixCelSet...
 Updating AffymetrixCelSet...
  Scanning for and applying sample annotation files...
   Loading all SampleAnnotationSet:s...
Identify all directories containing SAF files...
 All SAF files located:
 [1] annotationData/samples/
M7.saf
 [2] /nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/
aroma.affymetrix/annotationData/samples/HapMap270.saf


It found the  the M7.saf but also try to locate the other *saf files.

How to avoid this situation?  Thanks!



-- 
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
To unsubscribe and other options, go to http://www.aroma-project.org/forum/


Re: [aroma.affymetrix] AffymetrixCelSet$byName failed in aroma.affymetrix v2.1.0

2011-05-05 Thread Henrik Bengtsson
Hi,

unfortunately there is no option to turn off locating *.saf files part
of the package installation (I'll see if I can add one for the next
release).  However, it's strange if that would be the cause for you
problem, but on the other hand strange things happens all the time.

For troubleshooting, see what the following does:

sas - SampleAnnotationSet$loadAll(verbose=-5);
print(sas);

for (kk in seq(sas)) {
  saf - getFile(sas, kk);
  print(saf);
  df - readDataFrame(saf, verbose=-5);
  str(df);
} # for (kk ...)

Do you get an error?  If so, for what file?  Please provide a
traceback() report upon errors.  Does the other SAF files work, i.e.
if you try manually with different 'kk':s will they load?

Cheers,

Henrik

On Thu, May 5, 2011 at 9:00 AM, richland yiping.f...@gmail.com wrote:
 Hi,list,


  Here is my basic set up under my current working directory:~/project/

 rawData/M7/GenomeWideSNP_6/
 23..CEL  SJO023-snp6.CEL  25-snp6.CEL,26-snp6.CEL ...

 ==
 annotationData/chipTypes/GenomeWideSNP_6/

 GenomeWideSNP_6,Full.cdf
 GenomeWideSNP_6,Full,na30,hg18,HB20100215.ufl
 GenomeWideSNP_6,Full,na30,hg18,HB20100215.ugp
 GenomeWideSNP_6,HB20080710.acs

 I don't need sample information so there is no samples/ directory
 under annotationData

 I'm using R/2.12.0,  aroma.affymetrix v2.1.0 (2011-04-08)

 #
 ibrary(aroma.affymetrix)
 verbose - Arguments$getVerbose(-8)
 timestampOn(verbose)

 chipType - GenomeWideSNP_6

 cdf- AffymetrixCdfFile$byChipType(chipType,tags=Full)

 print(cdf) # ok

 dataSetName-M7;
 cs - AffymetrixCelSet$byName(dataSetName,
                             cdf=cdf,  verbose=-10)
 failed:

 it found all  6 cell files, but keeps looking form saf file in /
 nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/aroma.affymetrix/
 annotationData/samples/HapMap270.saf



 
 Trying path #1 of 1...
  Path: rawData/M7/GenomeWideSNP_6
  Defining AffymetrixCelSet from files...
   Defining an AffymetrixCelSet object from files...
    Path: rawData/M7/GenomeWideSNP_6
    Pattern: [.](c|C)(e|E)(l|L)$
    File class: AffymetrixCelFile
    Scanning directory for files...
     Found 6 files/directories.
     Found 6 files.
    Scanning directory for files...done
    Defining 6 files...
 1, 2, 3, 4, 5, 6,
    Defining 6 files...done
    Allocating a new AffymetrixCelSet instance...
     Arguments:
     Number of files: 6
      list()
    Allocating a new AffymetrixCelSet instance...done
    Updating newly allocated AffymetrixCelSet...
     Updating AffymetrixCelSet...
      Scanning for and applying sample annotation files...
       Loading all SampleAnnotationSet:s...
        Identify all directories containing SAF files...
         All SAF files located:
         [1] /nfs_exports/apps/64-bit/gnu-apps/R/libraries/2.12.0/
 aroma.affymetrix/annotationData/samples/HapMap270.saf

 Path (to the first file): /nfs_exports/apps/64-bit/gnu-apps/R/
 libraries/2.12.0/aroma.affymetrix/annotationData/samples
     Total file size: 0.03 MB
     RAM: 0.00MB
    Scanning for and applying sample annotation files...done
   Updating AffymetrixCelSet...done
  Defining AffymetrixCelSet from files...done
  Data set could not be setup for this path, because:
  cannot open the connection
  Trying path #1 of 1...done
 Error in list(`AffymetrixCelSet$byName(dataSetName, cdf = cdf, verbose
 = -10)` = environment,  :

 [2011-05-05 10:46:03] Exception: Failed to setup a data set for any of
 1 data directories located.
  at throw(Exception(...))
  at throw.default(sprintf(Failed to setup a data set for any of %d
 data direct
  at throw(sprintf(Failed to setup a data set for any of %d data
 directories lo
  at method(static, ...)
  at AffymetrixCelSet$byName(dataSetName, cdf = cdf, verbose = -10)
 Calls: Anonymous ... method - throw - throw.default - throw -
 throw.Exception
 Setting up AffymetrixCelSet by name...done
 Execution halted

 ===
 I also tried to make a samples/ directory under annotationData/ ans
 made a file called M7.saf. it also failed.

 [1] rawData/M7/GenomeWideSNP_6
  Trying path #1 of 1...
  Path: rawData/M7/GenomeWideSNP_6
  Defining AffymetrixCelSet from files...
   Defining an AffymetrixCelSet object from files...
    Path: rawData/M7/GenomeWideSNP_6
    Pattern: [.](c|C)(e|E)(l|L)$
    File class: AffymetrixCelFile
    Scanning directory for files...
     Found 6 files/directories.
     Found 6 files.
    Scanning directory for files...done
    Defining 6 files...
 1, 2, 3, 4, 5, 6,
    Defining 6 files...done
    Allocating a new AffymetrixCelSet instance...
     Arguments:
     Number of files: 6
      list()
    Allocating a new AffymetrixCelSet instance...done
    Updating newly allocated AffymetrixCelSet...
     Updating AffymetrixCelSet...
      Scanning for and applying sample annotation files...
       Loading all SampleAnnotationSet:s...
        Identify all directories containing SAF files...
         All SAF files located:
         [1] annotationData/samples/
 M7.saf