readChp in affxparser
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@gabor-csardi-3111
Last seen 8.2 years ago
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
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@gabor-csardi-2729
Last seen 2.0 years ago
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;LC_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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
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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;LC _NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDEN TIFICATION=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
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