Question: About goTools and multiple chips
0
14.8 years ago by
Hello all! Since I have seen many threads about ontoTools and Juerg Straubhaar in an e-mail said that : I tried this: >ontoCompare(namesList,probeType=c("moe430a","moe430b"), plot=TRUE) >[1] "Starting ontoCompare..." >Error: val; The reply from John Zhang said that he is missing the moe4302 package. Maybe in his case is true but I have a similar error message when trying my list from moe430 chip. The problem as I see it is that ontoToold DOES NOT accept probeType=c("moe430a","moe430b"), you have to pick either one or the other. In my case: ontoCompare(glists[1],probeType=c("moe430a","moe430b"),plot=T) [1] "Starting ontoCompare..." Error: value for "1419791_at" not found > xx<-as.list(moe430bSYMBOL) > xx["1419791_at"] $"1419791_at" [1] "Zhx3" As you can see the probe is in the moe430b chip. I think it is a very good idea to modify the code such that it can do GO for both chips. This problem renders ontoTools rather obsolete since one would have to do the GO for each chip separately, merge the output and plot. I would use it... but until the problem is fixed I wrote my own code :) Radu -- Dr. Radu Dobrin Department of Molecular Biology Princeton University Washington Road Princeton, NJ 08544-1014 Phone: 609-258-5657 E-mail: rdobrin@molbio.princeton.edu go moe430b probe ontotools • 429 views ADD COMMENTlink modified 14.8 years ago by Paquet, Agnes500 • written 14.8 years ago by Radu Dobrin40 Answer: About goTools and multiple chips 0 14.8 years ago by Paquet, Agnes500 Paquet, Agnes500 wrote: Dear Radu and Juerg, At the moment, goTools accepts either probe Ids from a single Affy chip or GO ids. When using data from different chips, the easiest way to use goTools is to convert your Affy ids into GO ids, then use these GO ids as argument (make sure you are using a version of goTools > =1.0.4 as we found a bug in earlier versions). Best, Agnes -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Radu Dobrin Sent: Wednesday, February 09, 2005 6:10 AM To: bioconductor@stat.math.ethz.ch Subject: [BioC] About goTools and multiple chips Hello all! Since I have seen many threads about ontoTools and Juerg Straubhaar in an e-mail said that : I tried this: >ontoCompare(namesList,probeType=c("moe430a","moe430b"), plot=TRUE) >[1] "Starting ontoCompare..." >Error: val; The reply from John Zhang said that he is missing the moe4302 package. Maybe in his case is true but I have a similar error message when trying my list from moe430 chip. The problem as I see it is that ontoToold DOES NOT accept probeType=c("moe430a","moe430b"), you have to pick either one or the other. In my case: ontoCompare(glists[1],probeType=c("moe430a","moe430b"),plot=T) [1] "Starting ontoCompare..." Error: value for "1419791_at" not found > xx<-as.list(moe430bSYMBOL) > xx["1419791_at"]$"1419791_at" [1] "Zhx3" As you can see the probe is in the moe430b chip. I think it is a very good idea to modify the code such that it can do GO for both chips. This problem renders ontoTools rather obsolete since one would have to do the GO for each chip separately, merge the output and plot. I would use it... but until the problem is fixed I wrote my own code :) Radu -- Dr. Radu Dobrin Department of Molecular Biology Princeton University Washington Road Princeton, NJ 08544-1014 Phone: 609-258-5657 E-mail: rdobrin@molbio.princeton.edu _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor