[BioC] readChp in affxparser

[Henrik Bengtsson]

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, Gábor Csárdi <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, Gábor Csárdi <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_IDENTIFICATION=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, Gábor Csárdi <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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