Hi Henrik,
I edited the CDF to make NumberOfUnits=18909 and convertCdf worked
successfully.
Thanks a lot for the help!
Ying
On Jul 13, 4:43 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> 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)
> >> >> >> 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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> >> > --
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