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
>
> > --
> > 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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> > Hide quoted text -
>
> - Show quoted text -
--
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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