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Question: question of justRMA on exon array
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gravatar for Jack Luo
4.8 years ago by
Jack Luo340
Jack Luo340 wrote:
Hi, I am trying to RMA normalize a bunch of exon arrays. I thought this is as easy as what I have done with the gene 1.0 ST array by using justRMA. However, it has the error information: *.CEL does not seem to have cdf information I provided the path of the CDF I downloaded from Affy website, but it does not help. Any clues? Thanks a lot, -Jack [[alternative HTML version deleted]]
ADD COMMENTlink modified 4.8 years ago by James W. MacDonald45k • written 4.8 years ago by Jack Luo340
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gravatar for James W. MacDonald
4.8 years ago by
United States
James W. MacDonald45k wrote:
Hi Jack, On 1/14/2013 4:30 PM, Jack Luo wrote: > Hi, > > I am trying to RMA normalize a bunch of exon arrays. I thought this is as > easy as what I have done with the gene 1.0 ST array by using justRMA. > However, it has the error information: > > *.CEL does not seem to have cdf information > > I provided the path of the CDF I downloaded from Affy website, but it does > not help. Where did you get the idea that would work? Note that I am not trying to be critical, I am really interested in knowing. Anyway, that's not how things work. You can't just point to an Affy CDF and have things work out, you have to install a cdf package that was built for R. Normally this is an automagic install, but in this case there isn't a pre-built cdf. I don't recall why I have never built a cdf package for this array, but I just tried and it segfaults, so that is likely why. Well, that and the fact that the affy package was never intended to be used with these arrays so I have a pre-existing antipathy towards doing this. But if you insist, you can get alternate versions here: http://dmp.i-med.ac.at/index.php/en/resources/bioinfo-menu-custom-cdf- jumi Download the CDF R Package, and then install using install.packages("huex10stv268cdf_0.2.0.tar.gz", type="source", repos = NULL) or you can just add cdfname = "huex10stv2hsentrezgcdf" to your call to justRMA() to get the MBNI remapped version. You can get CDFs mapped based on any number of annotations, see for instance the Version 16 arrays here: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF _download.asp Or you could do what IMO you should be doing anyway, and install oligo or xps and process with software that is intended for these arrays. Best, Jim > > Any clues? > > Thanks a lot, > > -Jack > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 4.8 years ago by James W. MacDonald45k
Hi James, Thanks for your reply. No, I did not get that idea from anywhere, I am a newbie to Exon array, although I have analyzed a lot of Gene 1.0 ST array. I thought Exon array should be very similar to Gene ST array, that's why I thought justRMA should work for them (since justRMA works fine for Gene ST array). I'll give a shot on what you proposed to see how it works. Thanks again, -Jack On Mon, Jan 14, 2013 at 5:20 PM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Jack, > > > On 1/14/2013 4:30 PM, Jack Luo wrote: > >> Hi, >> >> I am trying to RMA normalize a bunch of exon arrays. I thought this is as >> easy as what I have done with the gene 1.0 ST array by using justRMA. >> However, it has the error information: >> >> *.CEL does not seem to have cdf information >> >> I provided the path of the CDF I downloaded from Affy website, but it does >> not help. >> > > Where did you get the idea that would work? Note that I am not trying to > be critical, I am really interested in knowing. > > Anyway, that's not how things work. You can't just point to an Affy CDF > and have things work out, you have to install a cdf package that was built > for R. Normally this is an automagic install, but in this case there isn't > a pre-built cdf. > > I don't recall why I have never built a cdf package for this array, but I > just tried and it segfaults, so that is likely why. Well, that and the fact > that the affy package was never intended to be used with these arrays so I > have a pre-existing antipathy towards doing this. But if you insist, you > can get alternate versions here: > > http://dmp.i-med.ac.at/index.**php/en/resources/bioinfo-menu-** > custom-cdf-jumi<http: dmp.i-med.ac.at="" index.php="" en="" resources="" bioinfo-menu-custom-cdf-jumi=""> > > Download the CDF R Package, and then install using > > install.packages("**huex10stv268cdf_0.2.0.tar.gz", type="source", repos = > NULL) > > or you can just add > > cdfname = "huex10stv2hsentrezgcdf" > > to your call to justRMA() to get the MBNI remapped version. You can get > CDFs mapped based on any number of annotations, see for instance the > Version 16 arrays here: > > http://brainarray.mbni.med.**umich.edu/Brainarray/Database/** > CustomCDF/CDF_download.asp<http: brainarray.mbni.med.umich.edu="" brai="" narray="" database="" customcdf="" cdf_download.asp=""> > > Or you could do what IMO you should be doing anyway, and install oligo or > xps and process with software that is intended for these arrays. > > Best, > > Jim > > > >> Any clues? >> >> Thanks a lot, >> >> -Jack >> >> [[alternative HTML version deleted]] >> >> ______________________________**_________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.e="" thz.ch="" mailman="" listinfo="" bioconductor=""> >> Search the archives: http://news.gmane.org/gmane.** >> science.biology.informatics.**conductor<http: news.gmane.org="" gmane="" .science.biology.informatics.conductor=""> >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]
ADD REPLYlink written 4.8 years ago by Jack Luo340
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