[BioC] problems when using "readCcg" in "affxparser" to parse .CNCHP file

[cstrato]

Dear Tao,

This is interesting since I was not able to use "apt-chp-to-txt" thus I 
had to use the APT option "--text-output true" to get the txt files.

Thank you for the tip to import the APT generated .cnchp files into 
Genotyping Console first, I will try it.

Best regards
Christian

Shi, Tao wrote:
> Hi Christian,
>
> Thanks for your comment!
>
> I found out that you can use "apt-chp-to-txt" to convert the .cnchp 
> files to txt files and then read them into R.
>
> I was able to load the APT generated .cnchp files into Genotyping 
> Console and using its browser to view the data.
>
> best,
>
> ...Tao
>
>
> ------------------------------------------------------------------------
> *From:* cstrato <cstrato at aon.at>
> *To:* "Shi, Tao" <shidaxia at yahoo.com>
> *Cc:* bioconductor at stat.math.ethz.ch
> *Sent:* Fri, January 29, 2010 11:23:22 AM
> *Subject:* Re: [BioC] problems when using "readCcg" in "affxparser" to 
> parse .CNCHP file
>
> Dear Tao,
>
> This is not an answer to your question but  a comment:
> Using APT I have created  *.CNCHP files and wanted to import these files
> into the Affy Integrated Genome Browser. Although the IGB could display
> the name of the files, it was not able to display the results.
> Thus it seems that .CNCHP files created with APT are not compatible to
> .CNCHP files created with the Genotyping Console, which is really sad
> and may be the reason for your problem.
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._._._
> C.h.r.i.s.t.i.a.n  S.t.r.a.t.o.w.a
> V.i.e.n.n.a          A.u.s.t.r.i.a
> e.m.a.i.l:        cstrato at aon.at <http://aon.at>
> _._._._._._._._._._._._._._._._._._
>
>
> Shi, Tao wrote:
> > Hi list,
> >
> > I found the following problem when using "readCcg" in affxparser 
> package to parse .CNCHP files.
> >
> > The function worked fine with the .CNCHP files generated from Affy 
> Genotyping Console, but failed on those generated using Affy Power 
> Tools (please see the error below).  I'm using R 2.10.1 and affxparser 
> 1.18.0 on Win XP.  You help is really appreciated!
> >
> > ======================================================
> > Error in dim(value) <- c(nchars, nbrOfRows) :
> >  dims [product 16320969] do not match the length of object [25388174]
> > ======================================================
> >
> >
> > Thanks.
> >
> > ...Tao
> >
> >
> >     
> >     [[alternative HTML version deleted]]
> >
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>
>