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 13.72 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 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/ > -- 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/
