Hi, a very late follow up: I've committed your patch to both the release and the devel branches of affxparser. The new version should be available any day. Thanks Henrik On Fri, Oct 31, 2008 at 2:59 PM, G?bor Cs?rdi <csardi.gabor at="" gmail.com=""> wrote: > OK, it seems that this was a bug in affxparser, here is a tiny patch > that seems to be good according to my test and my rather incomplete > knowledge about these files: > > --- affxparser-1.15.orig/src/R_affx_chp_parser.cpp 2008-10-22 > 01:33:12.000000000 +0200 > +++ affxparser-1.15/src/R_affx_chp_parser.cpp 2008-10-31 > 14:54:31.000000000 +0100 > @@ -778,7 +778,7 @@ > if(nGeno > 0) nDataTypes++; > if(nGenoC > 0) nDataTypes++; > > - lstNbr = nDataTypes + 6; > + lstNbr = nDataTypes + 7; > PROTECT(lst = NEW_LIST(lstNbr)); > PROTECT(nms = NEW_CHARACTER(lstNbr)); > nprotect+=2; > > Best, > Gabor > > On Fri, Oct 31, 2008 at 12:39 PM, G?bor Cs?rdi <csardi.gabor at="" gmail.com=""> wrote: >> Hmmm, I am sorry for not including these in the original post: >> >> R version 2.8.0 (2008-10-20) >> i486-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] affxparser_1.15.0 >> >> loaded via a namespace (and not attached): >> [1] tools_2.8.0 >> >> On Fri, Oct 31, 2008 at 12:34 PM, G?bor Cs?rdi <gabor.csardi at="" unil.ch=""> wrote: >>> Dear All, I'm trying to read a CHP file produced by Affymetrix >>> Genotyping Console software. It seems that readChp can only read the >>> summary information from the file, is that correct, or am I doing >>> something wrong? Is there another package or piece of software that >>> can read these files? >>> >>> Thanks, Gabor >>> -- >>> Gabor Csardi <gabor.csardi at="" unil.ch=""> UNIL DGM >>> >> >> -- >> Gabor Csardi <gabor.csardi at="" unil.ch=""> UNIL DGM >> > > > > -- > Gabor Csardi <gabor.csardi at="" unil.ch=""> UNIL DGM > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >