problems when using "readCcg" in "affxparser" to parse .CNCHP file
1
0
Entering edit mode
Shi, Tao ▴ 720
@shi-tao-199
Last seen 7.1 years ago
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]]
affy affy • 641 views
ADD COMMENT
0
Entering edit mode
cstrato ★ 3.9k
@cstrato-908
Last seen 3.9 years ago
Austria
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 _._._._._._._._._._._._._._._._._._ 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 > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >
ADD COMMENT
0
Entering edit mode
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@aon.at> Cc: bioconductor@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 _._._._._._._._._._._._._._._._._._ Shi, Tao wrote: > Hi list, > > I found the following problem when using "readCcg" in affxparser package to parse .CNCHP files. > [[elided Yahoo spam]] > > ====================================================== > 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@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]
ADD REPLY
0
Entering edit mode
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 > > > > > >
ADD REPLY

Login before adding your answer.

Traffic: 173 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6