Question: MOE430 A and B
0
gravatar for peter robinson
15.7 years ago by
peter robinson300 wrote:
Dear List members, I would like to use the affy package to analyze data from MOE430A and -B chips. I tried to read in data from both types of chips at once using data <- ReadAffy(widget=T) and then reading in 3 MOE430A and 3 MOE430B CEL files. I got the error message: "Cel file does not seem to beo of 430MOEA type" when the script tried to input data from a 430MOEB Cel file. I had imported the CDF and annotation packages for both types of chip. I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system. Thanks for any advice/tips! Peter
moe430a moe430b cdf affy • 716 views
ADD COMMENTlink modified 15.7 years ago by Aedin Culhane310 • written 15.7 years ago by peter robinson300
Answer: MOE430 A and B
0
gravatar for rgentleman
15.7 years ago by
rgentleman5.5k
United States
rgentleman5.5k wrote:
You need to deal with each type of chip separately, most of the normalization/expression estimation procedures work using the values for the same probes across chips. So it makes no sense to put in two different types of chips, you need to normalize and compute expression measure separately - there are some exceptions, in that you could try to use common probes across both chip types. Robert On Mon, Mar 15, 2004 at 01:20:25PM +0100, peter robinson wrote: > Dear List members, > > I would like to use the affy package to analyze data from MOE430A and -B > chips. I tried to read in data from both types of chips at once using > data <- ReadAffy(widget=T) > and then reading in 3 MOE430A and 3 MOE430B CEL files. > I got the error message: > "Cel file does not seem to beo of 430MOEA type" when the script tried to input > data from a 430MOEB Cel file. I had imported the CDF and annotation packages > for both types of chip. > I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system. > > Thanks for any advice/tips! > > Peter > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | | Harvard School of Public Health email: rgentlem@jimmy.harvard.edu | +--------------------------------------------------------------------- ------+
ADD COMMENTlink written 15.7 years ago by rgentleman5.5k
Answer: MOE430 A and B
0
gravatar for Ben Bolstad
15.7 years ago by
Ben Bolstad1.1k
Ben Bolstad1.1k wrote:
you need to read in the type A and type B files into separate affybatch objects. eg my.Data.A <- ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel")) my.Data.B <- ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel")) Ben On Mon, 2004-03-15 at 04:20, peter robinson wrote: > Dear List members, > > I would like to use the affy package to analyze data from MOE430A and -B > chips. I tried to read in data from both types of chips at once using > data <- ReadAffy(widget=T) > and then reading in 3 MOE430A and 3 MOE430B CEL files. > I got the error message: > "Cel file does not seem to beo of 430MOEA type" when the script tried to input > data from a 430MOEB Cel file. I had imported the CDF and annotation packages > for both types of chip. > I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system. > > Thanks for any advice/tips! > > Peter > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
ADD COMMENTlink written 15.7 years ago by Ben Bolstad1.1k
Hi I am having problems using annaffy GO (aafGO) annotations on these chips? I have updated my chip annotation files, and GO library, but still get > a<-aafGO(rownames(chipA), "moe430a") Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found Thanks for your help, Aedin -----Original Message----- From: bioconductor-bounces+aedin.culhane=ucd.ie@stat.math.ethz.ch [mailto:bioconductor-bounces+aedin.culhane=ucd.ie@stat.math.ethz.ch]On Behalf Of Ben Bolstad Sent: 15 March 2004 14:17 To: peter robinson Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] MOE430 A and B you need to read in the type A and type B files into separate affybatch objects. eg my.Data.A <- ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel")) my.Data.B <- ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel")) Ben On Mon, 2004-03-15 at 04:20, peter robinson wrote: > Dear List members, > > I would like to use the affy package to analyze data from MOE430A and -B > chips. I tried to read in data from both types of chips at once using > data <- ReadAffy(widget=T) > and then reading in 3 MOE430A and 3 MOE430B CEL files. > I got the error message: > "Cel file does not seem to beo of 430MOEA type" when the script tried to input > data from a 430MOEB Cel file. I had imported the CDF and annotation packages > for both types of chip. > I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system. > > Thanks for any advice/tips! > > Peter > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD REPLYlink written 15.7 years ago by Aedin Culhane310
I am getting exactly the same error in aafGO: > a<-aafGO(probeids,"moe430a") Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found This is when using version 1.5.0 of the moe430a metadata package. In a different machine with version 1.4.0 this works alright. annaffy version is 1.0.3 in both. Thanks Jose On Mon, 2004-03-15 at 17:04, Aedin wrote: > Hi > I am having problems using annaffy GO (aafGO) annotations on these chips? I > have updated my chip annotation files, and GO library, but still get > > > a<-aafGO(rownames(chipA), "moe430a") > Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found > > Thanks for your help, > Aedin > > -----Original Message----- > From: bioconductor-bounces+aedin.culhane=ucd.ie@stat.math.ethz.ch > [mailto:bioconductor- bounces+aedin.culhane=ucd.ie@stat.math.ethz.ch]On > Behalf Of Ben Bolstad > Sent: 15 March 2004 14:17 > To: peter robinson > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] MOE430 A and B > > > you need to read in the type A and type B files into separate affybatch > objects. > > eg > > my.Data.A <- > ReadAffy(filenames=c("blahA1.cel","blahA2.cel","blahA3.cel")) > > my.Data.B <- > ReadAffy(filenames=c("blahB1.cel","blahB2.cel","blahB3.cel")) > > Ben > > > > > > > On Mon, 2004-03-15 at 04:20, peter robinson wrote: > > Dear List members, > > > > I would like to use the affy package to analyze data from MOE430A and -B > > chips. I tried to read in data from both types of chips at once using > > data <- ReadAffy(widget=T) > > and then reading in 3 MOE430A and 3 MOE430B CEL files. > > I got the error message: > > "Cel file does not seem to beo of 430MOEA type" when the script tried to > input > > data from a 430MOEB Cel file. I had imported the CDF and annotation > packages > > for both types of chip. > > I am using R 1.81, Bioconductor 1.3 on a SuSe 8.1 linux system. > > > > Thanks for any advice/tips! > > > > Peter > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > -- > Ben Bolstad <bolstad@stat.berkeley.edu> > http://www.stat.berkeley.edu/~bolstad > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- Jose Duarte <jose.duarte@anat.ox.ac.uk>
ADD REPLYlink written 15.7 years ago by Jose Duarte100
> This is when using version 1.5.0 of the moe430a metadata package. In a > different machine with version 1.4.0 this works alright. annaffy version > is 1.0.3 in both. The problem appears to be that there was a difference between the 1.4.x series of metadata packages and the 1.5.x series which breaks annaffy-release. Going back to an earlier message of mine about how we just recently split the release/devel metadata packages, this was exactly the sort of problem that caused that -> as our metadata packages change on a release cycle that isn't the same as our software, if we are only offering one version of the metadata, it might cause problems with previously released software. The problem with the split/rollback a few days ago was that we had already been offering the 1.5.0 packages for quite some time and did not want roll back further to the 1.4.x series of packages. One solution, if it is feasible for your needs, is to use the devel versions of the packages (although in many cases this will require you to be using R-1.9.0, currently in alpha stage -> although I believe that annaffy does not have this restriction). In the meantime, I will look into the possibility of also providing the 1.4.x data packages. Thanks -J
ADD REPLYlink written 15.7 years ago by Jeff Gentry3.9k
Thanks, I tried this, but the dev version of annaffy requires utils. So a half one version, half the next doesn't work. So I might just download all the dev version. Aedin -----Original Message----- From: Jeff Gentry [mailto:jgentry@jimmy.harvard.edu] Sent: 16 March 2004 17:23 To: Jose Duarte Cc: Aedin; bioconductor@stat.math.ethz.ch Subject: RE: [BioC] MOE430 A and B - bug? > This is when using version 1.5.0 of the moe430a metadata package. In a > different machine with version 1.4.0 this works alright. annaffy version > is 1.0.3 in both. The problem appears to be that there was a difference between the 1.4.x series of metadata packages and the 1.5.x series which breaks annaffy-release. Going back to an earlier message of mine about how we just recently split the release/devel metadata packages, this was exactly the sort of problem that caused that -> as our metadata packages change on a release cycle that isn't the same as our software, if we are only offering one version of the metadata, it might cause problems with previously released software. The problem with the split/rollback a few days ago was that we had already been offering the 1.5.0 packages for quite some time and did not want roll back further to the 1.4.x series of packages. One solution, if it is feasible for your needs, is to use the devel versions of the packages (although in many cases this will require you to be using R-1.9.0, currently in alpha stage -> although I believe that annaffy does not have this restriction). In the meantime, I will look into the possibility of also providing the 1.4.x data packages. Thanks -J
ADD REPLYlink written 15.7 years ago by Aedin Culhane310
It did the trick for me. I installed the dev version of annaffy which also required the latest annotate. After upgrading both everything worked fine. Thanks for all your help Jose On Tue, 2004-03-16 at 17:25, Aedin wrote: > Thanks, > I tried this, but the dev version of annaffy requires utils. So a half one > version, half the next doesn't work. So I might just download all the dev > version. > Aedin > > -----Original Message----- > From: Jeff Gentry [mailto:jgentry@jimmy.harvard.edu] > Sent: 16 March 2004 17:23 > To: Jose Duarte > Cc: Aedin; bioconductor@stat.math.ethz.ch > Subject: RE: [BioC] MOE430 A and B - bug? > > > > This is when using version 1.5.0 of the moe430a metadata package. In a > > different machine with version 1.4.0 this works alright. annaffy version > > is 1.0.3 in both. > > The problem appears to be that there was a difference between the 1.4.x > series of metadata packages and the 1.5.x series which breaks > annaffy-release. > > Going back to an earlier message of mine about how we just recently split > the release/devel metadata packages, this was exactly the sort of problem > that caused that -> as our metadata packages change on a release cycle > that isn't the same as our software, if we are only offering one version > of the metadata, it might cause problems with previously released > software. > > The problem with the split/rollback a few days ago was that we had already > been offering the 1.5.0 packages for quite some time and did not want roll > back further to the 1.4.x series of packages. > > One solution, if it is feasible for your needs, is to use the devel > versions of the packages (although in many cases this will require you to > be using R-1.9.0, currently in alpha stage -> although I believe that > annaffy does not have this restriction). In the meantime, I will look > into the possibility of also providing the 1.4.x data packages. > > Thanks > -J
ADD REPLYlink written 15.7 years ago by Jose Duarte100
Answer: MOE430 A and B
0
gravatar for Aedin Culhane
15.7 years ago by
Aedin Culhane310
Aedin Culhane310 wrote:
Thanks, I updated the packages annaffy and annotate (install.packages("annaffy", CRAN=getOption("BIOC"))), but still get errors > anncols<-aaf.handler() > anntableB<-aafTableAnn(pB, "moe430b", anncols) Error in if (!is.na(go[1])) { : argument is of length zero In addition: Warning message: is.na() applied to non-(list or vector) in: is.na(go[1]) > anntableA<-aafTableAnn(pA, "moe430a", anncols) Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found Thanks for your help Aedin -----Original Message----- From: Robert Gentleman [mailto:rgentlem@jimmy.harvard.edu] Sent: 15 March 2004 23:16 To: Aedin Subject: Re: [BioC] MOE430 A and B On Mon, Mar 15, 2004 at 05:04:52PM +0000, Aedin wrote: > Hi > I am having problems using annaffy GO (aafGO) annotations on these chips? I > have updated my chip annotation files, and GO library, but still get > > > a<-aafGO(rownames(chipA), "moe430a") > Error in exists(num, GOBPID2TERM) : Object "GOBPID2TERM" not found > Hi there have been some changes to the GO package and these mappings are no longer needed (and so no longer included). I think if you get a more recent version of annaffy it may work. try install.packages("annaffy") and then see if that has made things better Robert +--------------------------------------------------------------------- ------ +
ADD COMMENTlink written 15.7 years ago by Aedin Culhane310
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