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.
Ying
> library("affxparser")
> pathname <- "HTHGU133PlusPM_Hs_ENTREZG.cdf"
> file.info(pathname)$size
[1] 23933996
> digest::digest(file=pathname)
[1] "a3cbf4eab4048e048a622ea68fd5e02b"
> convertCdf(pathname, "HTHGU133PlusPM_Hs_ENTREZG,Binary.cdf", verbose=TRUE)
Reading CDF header...
Reading CDF header...done
Reading CDF QC units...
On Jul 13, 3:30 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:
> My guess is that your CDF is corrupt/incomplete (interrupted
> download?). I downloaded
>
> http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/14...
>
> extracted the ZIP file and got:
>
> > library("affxparser")
> > pathname <- "HTHGU133B_Hs_ENTREZG.cdf"
> > file.info(pathname)$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
>
> >> > --
> >> > 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
> >> > websitehttp://www.aroma-project.org/.
> >> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> >> > To unsubscribe and other options, go
> >> > tohttp://www.aroma-project.org/forum/-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.
>
> > You received this message because you are subscribed to the Google Groups
> > "aroma.affymetrix" group with websitehttp://www.aroma-project.org/.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go tohttp://www.aroma-project.org/forum/-
> > 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.
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/
