Hi George, I've never made a probe package either? Did you try searching the BioC archives for "make probe package"? http://dir.gmane.org/gmane.science.biology.informatics.conductor Also, you forgot to post to the BioC list as well! Cheers, Jenny At 08:40 AM 3/31/2010, George Roberts III wrote: >Hi Jenny, > >I installed the .CDF package for my chips but still don't know how >to make a cdfprobe package and couldn't find any further info. > >Thanks for your help, >George > >On Sat, Jan 23, 2010 at 11:58 PM, George Roberts ><<mailto:groberts0429@gmail.com>groberts0429@gmail.com> wrote: >Hi Jenny, > >Sorry for not posting in the BioC list, I will in the future; I >found the URL where you posted the previous email but don't know how >to reply to that thread so I replied to this email instead. > >I spoke with the designers of the custom chip to find some insight >into the "NA" issue. All of the "NA" values were traced to a series >of probes that consist of only a single PM probe for each gene. They >were analyzed with GCOS and none gave "NA"; all gave a number. The >individual who performed the first analysis had no further insight >into whey R might have behaved this way. I want to exclude these >probes from my analysis in any event. > >Thanks for pointing out that this error had to do with not >installing the .CDF package. I had loaded the .CDF environment in >the belief that it would be enough. Installing the .CDF package and >.CDFprobe package will be my next step. > >Thank you very much for your help, >George > > >On Tue, Jan 19, 2010 at 9:38 AM, Jenny Drnevich ><<mailto:drnevich@illinois.edu>drnevich@illinois.edu> wrote: >Hi George, > >Sorry I haven't been able to respond - I've been extremely busy. >It's actually better to post questions like this to the BioC list >instead of to one poster directly - you might get a more timely >response, and it's good to have the response in the archives so >other people can access it. Your error message is pretty simple - >you don't have package mpauta520274cdfprobe. I'm guessing this is a >custom Affy array, so in addition to the mpaut1a520274fcdf package, >you'll need a mpaut1a520274fprobe package to be able to use the >RemoveProbes function "as is" and other functions like gcrma(). I >forget off the top of my head what you need to do to make the probe >package, so perhaps others will comment. If you can't make the probe >package and only want to remove entire probe sets, then the code of >RemoveProbes might be able to be modified to work without the probe >package. Unfortunately, I won't have time for a couple of weeks to >look at it. Feel free to hack it all you want if you can! Sorry I >can't be of more help right now... > >Jenny > >P.S. What's going on with your scans that you are getting "NA" >values for individual probes? That's very odd! > > >At 05:48 PM 1/12/2010, George Roberts wrote: >>Dr. Drnevich, >> >>I would like to use your code >><https: stat.ethz.ch="" pipermail="" bioconductor="" 2008-september="" 024296.h="" tml="">https://stat.ethz.ch/pipermail/bioconductor/2008-September/024296. html >>to remove some probesets that are causing "NA" values resulting in >>errors. My CDF is "MPAUT1a520274F.CDF". I get the following error messages: >> >> > RemoveProbes(listOutProbes=NULL, listOutProbeSets=" >>+ 1415670_at >>+ 1415671_at >>+ 1415672_at >>+ ", cleancdf) >>Loading required package: mpaut1a520274fcdfcdf >>Loading required package: mpaut1a520274fcdfprobe >>Error in get(probepackagename) : >> object 'mpaut1a520274fcdfprobe' not found >>In addition: Warning messages: >>1: In library(package, lib.loc = lib.loc, character.only = TRUE, >>logical.return = TRUE, : >> there is no package called 'mpaut1a520274fcdfcdf' >>2: In library(package, lib.loc = lib.loc, character.only = TRUE, >>logical.return = TRUE, : >> there is no package called 'mpaut1a520274fcdfprobe' >> >>Thanks, >>George Roberts >>Wayne State University > >Jenny Drnevich, Ph.D. > >Functional Genomics Bioinformatics Specialist >W.M. Keck Center for Comparative and Functional Genomics >Roy J. Carver Biotechnology Center >University of Illinois, Urbana-Champaign > >330 ERML >1201 W. Gregory Dr. >Urbana, IL 61801 >USA > >ph: 217-244-7355 >fax: 217-265-5066 >e-mail: <mailto:drnevich@illinois.edu>drnevich@illinois.edu > > Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich@illinois.edu [[alternative HTML version deleted]]

The AnnotationDbi package contains a function makeProbePackage() that you can use to make probe packages. Best, Jim Jenny Drnevich wrote: > Hi George, > > I've never made a probe package either? Did you try searching the > BioC archives for "make probe package"? > > http://dir.gmane.org/gmane.science.biology.informatics.conductor > > Also, you forgot to post to the BioC list as well! > > Cheers, > Jenny > > At 08:40 AM 3/31/2010, George Roberts III wrote: >> Hi Jenny, >> >> I installed the .CDF package for my chips but still don't know how >> to make a cdfprobe package and couldn't find any further info. >> >> Thanks for your help, >> George >> >> On Sat, Jan 23, 2010 at 11:58 PM, George Roberts >> <<mailto:groberts0429 at="" gmail.com="">groberts0429 at gmail.com> wrote: >> Hi Jenny, >> >> Sorry for not posting in the BioC list, I will in the future; I >> found the URL where you posted the previous email but don't know how >> to reply to that thread so I replied to this email instead. >> >> I spoke with the designers of the custom chip to find some insight >> into the "NA" issue. All of the "NA" values were traced to a series >> of probes that consist of only a single PM probe for each gene. They >> were analyzed with GCOS and none gave "NA"; all gave a number. The >> individual who performed the first analysis had no further insight >> into whey R might have behaved this way. I want to exclude these >> probes from my analysis in any event. >> >> Thanks for pointing out that this error had to do with not >> installing the .CDF package. I had loaded the .CDF environment in >> the belief that it would be enough. Installing the .CDF package and >> .CDFprobe package will be my next step. >> >> Thank you very much for your help, >> George >> >> >> On Tue, Jan 19, 2010 at 9:38 AM, Jenny Drnevich >> <<mailto:drnevich at="" illinois.edu="">drnevich at illinois.edu> wrote: >> Hi George, >> >> Sorry I haven't been able to respond - I've been extremely busy. >> It's actually better to post questions like this to the BioC list >> instead of to one poster directly - you might get a more timely >> response, and it's good to have the response in the archives so >> other people can access it. Your error message is pretty simple - >> you don't have package mpauta520274cdfprobe. I'm guessing this is a >> custom Affy array, so in addition to the mpaut1a520274fcdf package, >> you'll need a mpaut1a520274fprobe package to be able to use the >> RemoveProbes function "as is" and other functions like gcrma(). I >> forget off the top of my head what you need to do to make the probe >> package, so perhaps others will comment. If you can't make the probe >> package and only want to remove entire probe sets, then the code of >> RemoveProbes might be able to be modified to work without the probe >> package. Unfortunately, I won't have time for a couple of weeks to >> look at it. Feel free to hack it all you want if you can! Sorry I >> can't be of more help right now... >> >> Jenny >> >> P.S. What's going on with your scans that you are getting "NA" >> values for individual probes? That's very odd! >> >> >> At 05:48 PM 1/12/2010, George Roberts wrote: >>> Dr. Drnevich, >>> >>> I would like to use your code >>> <https: stat.ethz.ch="" pipermail="" bioconductor="" 2008-september="" 024296="" .html="">https://stat.ethz.ch/pipermail/bioconductor/2008-September/02429 6.html >>> to remove some probesets that are causing "NA" values resulting in >>> errors. My CDF is "MPAUT1a520274F.CDF". I get the following error messages: >>> >>>> RemoveProbes(listOutProbes=NULL, listOutProbeSets=" >>> + 1415670_at >>> + 1415671_at >>> + 1415672_at >>> + ", cleancdf) >>> Loading required package: mpaut1a520274fcdfcdf >>> Loading required package: mpaut1a520274fcdfprobe >>> Error in get(probepackagename) : >>> object 'mpaut1a520274fcdfprobe' not found >>> In addition: Warning messages: >>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, >>> logical.return = TRUE, : >>> there is no package called 'mpaut1a520274fcdfcdf' >>> 2: In library(package, lib.loc = lib.loc, character.only = TRUE, >>> logical.return = TRUE, : >>> there is no package called 'mpaut1a520274fcdfprobe' >>> >>> Thanks, >>> George Roberts >>> Wayne State University >> Jenny Drnevich, Ph.D. >> >> Functional Genomics Bioinformatics Specialist >> W.M. Keck Center for Comparative and Functional Genomics >> Roy J. Carver Biotechnology Center >> University of Illinois, Urbana-Champaign >> >> 330 ERML >> 1201 W. Gregory Dr. >> Urbana, IL 61801 >> USA >> >> ph: 217-244-7355 >> fax: 217-265-5066 >> e-mail: <mailto:drnevich at="" illinois.edu="">drnevich at illinois.edu >> >> > > Jenny Drnevich, Ph.D. > > Functional Genomics Bioinformatics Specialist > W.M. Keck Center for Comparative and Functional Genomics > Roy J. Carver Biotechnology Center > University of Illinois, Urbana-Champaign > > 330 ERML > 1201 W. Gregory Dr. > Urbana, IL 61801 > USA > > ph: 217-244-7355 > fax: 217-265-5066 > e-mail: drnevich at illinois.edu > [[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 -- James W. MacDonald, M.S. Biostatistician Hildebrandt Lab 8220D MSRB III 1150 W. 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