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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch <mailto: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 > > > > > >