Re: [aroma.affymetrix] Re: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM

2011-07-13 Thread Henrik Bengtsson
My guess is that your CDF is corrupt/incomplete (interrupted
download?).  I downloaded

  
http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14.1.0/entrezg.download/HTHGU133PlusPM_Hs_ENTREZG_14.1.0.zip

extracted the ZIP file and got:

 library(affxparser)
 pathname - HTHGU133B_Hs_ENTREZG.cdf
 file.info(pathname)$size
[1] 16362942
 digest::digest(file=pathname)
[1] c0d0c13cc31c661c657633b7560988e3
 convertCdf(pathname, HTHGU133PlusPM_Hs_ENTREZG,Binary.cdf, verbose=TRUE)
Reading CDF header...
Reading CDF header...done
Reading CDF QC units...
Reading CDF QC units...done
Reading CDF units...
Reading CDF units...done
Writing CDF structure...
Timing for writeCdf():
   user  system elapsed
  13.720.03   13.76
Writing CDF structure...done
Comparing CDFs...
Comparing CDFs...
  CDF 1: ./HTHGU133B_Hs_ENTREZG.cdf
  CDF 2: ./HTHGU133PlusPM_Hs_ENTREZG,Binary.cdf
  Comparing CDF headers...
  Comparing CDF headers...done
  Comparing QC units...
  Comparing QC units...done
  Comparing units...
  Comparing units...done
Comparing CDFs...done
Comparing CDFs...done

/Henrik

On Wed, Jul 13, 2011 at 12:22 PM, sean nj njs...@gmail.com wrote:
 Hi Henrik,

 Thanks a lot for the help!

 What confused me is that I have no problem converting custom CDFs for
 HG-U133_Plus_2 chip. Below is the sessionInfo.

 Ying

 library(affxparser)
 sessionInfo()
 R version 2.13.0 (2011-04-13)
 Platform: i386-pc-mingw32/i386 (32-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] affxparser_1.24.0


 On Jul 13, 3:03 pm, Henrik Bengtsson henrik.bengts...@aroma-
 project.org wrote:
 Before anything else, what does:

  library(affxparser);
  sessionInfo();

 report?

 /Henrik

 PS. This is really a question for the Bioconductor list, because it is
 an 'affxparser' question and independent of the aroma framework, but
 let's deal with it here this time.



 On Wed, Jul 13, 2011 at 11:59 AM, sean nj njs...@gmail.com wrote:
  Hi guys,

  I was trying to convert BrainArray custom CDF for Affy HT_HG-
  U133_Plus_PM chip into binary CDF using convertCdf(). But every time I
  tried, I got the same error message:

  R for Windows GUI front-end:

  R for Windows GUI front-end has encountered a problem and needs to
  close.

  Error Signature:

  AppName:  rgui.exe
  AppVer:     2.130.55427.0
  ModName: affxparser.dll
  ModVer:    0.0.0.0
  OffSet:      0005207a

  In the R GUI window:

  library(affxparser)
  convertCdf(HTHGU133PlusPM_Hs_ENTREZG.cdf, 
  HTHGU133PlusPM_Hs_ENTREZG,Binary.cdf,
  + version = 4,force = TRUE,verbose=TRUE)
  Reading CDF header...
  Reading CDF header...done
  Reading CDF QC units...

  It hangs like that forever and nothing happens.

  I got this eror only when I tried to convert BrainArray's custom CDF
  for Affy HT_HG-U133_Plus_PM chip. I tried ENTREZG and REFSEQ versions
  of the custom CDF and got the same error message. I had no problem
  when converting the custom CDF for HG-U133_Plus_2 chip.

  Since R hangs every time the error message pops up, I could not
  provide any sessionInfo() info. My computer runs windows XP 32 bit
  with the latest R.

  Any suggestion?

  Thanks a lot for the help!

  Ying

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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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-- 
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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: convertCdf() crashes R while converting BrainArray custom CDF for Affy HT_HG-U133_Plus_PM

2011-07-13 Thread Henrik Bengtsson
Hi.

On Wed, Jul 13, 2011 at 12:58 PM, sean nj njs...@gmail.com wrote:
 Hi Henrik,

 Thanks a lot for the help.

 But I still have the same error. I think you tested
 HTHGU133B_Hs_ENTREZG.cdf, and I was talking about
 HTHGU133PlusPM_Hs_ENTREZG.cdf. I downloaded the same file several tmes
 now and still have the same error.

My mistake (as a future references please provide verbatim download
instructions/exact URLs so we avoid these simple mistakes).


 Ying


 library(affxparser)
 pathname - HTHGU133PlusPM_Hs_ENTREZG.cdf
 file.info(pathname)$size
 [1] 23933996
 digest::digest(file=pathname)
 [1] a3cbf4eab4048e048a622ea68fd5e02b
 convertCdf(pathname, HTHGU133PlusPM_Hs_ENTREZG,Binary.cdf, verbose=TRUE)
 Reading CDF header...
 Reading CDF header...done
 Reading CDF QC units...
[core dump]

I can reproduce this.  You get if you try to read any of the QC units
(or regular units), i.e. using readQcUnits() or
readUnits().

It is because that CDF is corrupt.  If you look at the header of the
file (using a text viewer), you find:

[CDF]
Version=GC3.0

[Chip]
Name=HTHGU133PlusPM
Rows=744
Cols=744
NumberOfUnits=0
MaxUnit=0
NumQCUnits=0
ChipReference=

Alternatively:

 str(readCdfHeader(pathname));
List of 12
 $ ncols  : int 744
 $ nrows  : int 744
 $ nunits : int 0
 $ nqcunits   : int 0
 $ refseq : chr 
 $ chiptype   : chr HTHGU133PlusPM_Hs_ENTREZG
 $ filename   : chr ./HTHGU133PlusPM_Hs_ENTREZG.cdf
 $ rows   : int 744
 $ cols   : int 744
 $ probesets  : int 0
 $ qcprobesets: int 0
 $ reference  : chr 

Note how it says there are zero units in the CDF, which is not true.
If you edit the CDF to say NumberOfUnits=18909 it works.

BrainArray folks (cc:ed), could you please fix this and also assert
that your other CDFs don't have this mistake.  The affxparser package
provides a useful tool for validating the correctness of your custom
CDF files.

/Henrik

PS. I would agree that affxparser should not core dump here.  However,
it is a rather particular file format error and the core dump occurs
in the Affymetrix Fusion SDK code that affxparser utilizes and there
is little we can to protect against this in affxparser.





 On Jul 13, 3:30 pm, Henrik Bengtsson henrik.bengts...@aroma-
 project.org wrote:
 My guess is that your CDF is corrupt/incomplete (interrupted
 download?).  I downloaded

  http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14...

 extracted the ZIP file and got:

  library(affxparser)
  pathname - HTHGU133B_Hs_ENTREZG.cdf
  file.info(pathname)$size
 [1] 16362942
  digest::digest(file=pathname)

 [1] c0d0c13cc31c661c657633b7560988e3 convertCdf(pathname, 
 HTHGU133PlusPM_Hs_ENTREZG,Binary.cdf, verbose=TRUE)

 Reading CDF header...
 Reading CDF header...done
 Reading CDF QC units...
 Reading CDF QC units...done
 Reading CDF units...
 Reading CDF units...done
 Writing CDF structure...
 Timing for writeCdf():
    user  system elapsed
   13.72    0.03   13.76
 Writing CDF structure...done
 Comparing CDFs...
 Comparing CDFs...
   CDF 1: ./HTHGU133B_Hs_ENTREZG.cdf
   CDF 2: ./HTHGU133PlusPM_Hs_ENTREZG,Binary.cdf
   Comparing CDF headers...
   Comparing CDF headers...done
   Comparing QC units...
   Comparing QC units...done
   Comparing units...
   Comparing units...done
 Comparing CDFs...done
 Comparing CDFs...done

 /Henrik



 On Wed, Jul 13, 2011 at 12:22 PM, sean nj njs...@gmail.com wrote:
  Hi Henrik,

  Thanks a lot for the help!

  What confused me is that I have no problem converting custom CDFs for
  HG-U133_Plus_2 chip. Below is the sessionInfo.

  Ying

  library(affxparser)
  sessionInfo()
  R version 2.13.0 (2011-04-13)
  Platform: i386-pc-mingw32/i386 (32-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] affxparser_1.24.0

  On Jul 13, 3:03 pm, Henrik Bengtsson henrik.bengts...@aroma-
  project.org wrote:
  Before anything else, what does:

   library(affxparser);
   sessionInfo();

  report?

  /Henrik

  PS. This is really a question for the Bioconductor list, because it is
  an 'affxparser' question and independent of the aroma framework, but
  let's deal with it here this time.

  On Wed, Jul 13, 2011 at 11:59 AM, sean nj njs...@gmail.com wrote:
   Hi guys,

   I was trying to convert BrainArray custom CDF for Affy HT_HG-
   U133_Plus_PM chip into binary CDF using convertCdf(). But every time I
   tried, I got the same error message:

   R for Windows GUI front-end:

   R for Windows GUI front-end has encountered a problem and needs to
   close.

   Error Signature:

   AppName:  rgui.exe
   AppVer:     2.130.55427.0
   ModName: affxparser.dll
   ModVer:    0.0.0.0
   OffSet:      0005207a

   In the R GUI window:

   library(affxparser)