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Question: Problem with invalid GO term in HyperGResult object - NOT solved
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gravatar for Seth Falcon
11.0 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
Jenny Drnevich <drnevich at="" uiuc.edu=""> writes: > Hi Seth, > > I had a problem earlier with an invalid GO term that was throwing up > an error. You advised to update all my packages, which I thought > solved the problem. However, the problem reappeared later when I reran > my script, and I've figured out the difference is what other packages > I have loaded. I have a complete R session below, where I first only > load GOstats, then call hyperGTest on a GOHyperGParams object, which > tests 1139 GO BP ids, and 44 have p < 0.001. Next I load > affycoretools, then call hyperGTest on the exact same object, which > now tests 1146 GO BP ids, and 46 have p < 0.001. Loading affycoretools > in turn loads package GO, which then masks many functions from package > GO.db - maybe this is where the problem is? I'm fine because I can > get the problematic GO term to disappear, but it seems like the > discordance between the packages is a bug. Yes, this is not as desired. But can you please try updating the GO package and see if this remains to be an issue :-) BTW, I believe this hasn't changed since your last update so I will recommend how to update: library(Biobase) update.packages(repos=biocReposList()) + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/
ADD COMMENTlink modified 11.0 years ago by Jenny Drnevich2.2k • written 11.0 years ago by Seth Falcon7.4k
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gravatar for Jenny Drnevich
11.0 years ago by
Jenny Drnevich2.2k
Jenny Drnevich2.2k wrote:
>Yes, this is not as desired. But can you please try updating the GO >package and see if this remains to be an issue :-) > >BTW, I believe this hasn't changed since your last update so I will >recommend how to update: > >library(Biobase) >update.packages(repos=biocReposList()) > >+ seth As of 2 minutes ago, these were the only packages that it updated... package 'affyio' successfully unpacked and MD5 sums checked package 'annaffy' successfully unpacked and MD5 sums checked package 'annotate' successfully unpacked and MD5 sums checked package 'AnnotationDbi' successfully unpacked and MD5 sums checked package 'biomaRt' successfully unpacked and MD5 sums checked package 'Category' successfully unpacked and MD5 sums checked package 'GOstats' successfully unpacked and MD5 sums checked package 'graph' successfully unpacked and MD5 sums checked package 'preprocessCore' successfully unpacked and MD5 sums checked ... and I'm still having the same problem. I also tried using biocLite("GO"), but it downloaded the same version I already had: 1.17.0. If there's a newer version, it's not available as a Windows binary. BTW, there is no package "GO" on the BioC website software listings for either BioC 2.0 or BioC 2.1... Thanks, Jenny >-- >Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >BioC: http://bioconductor.org/ >Blog: http://userprimary.net/user/ 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 uiuc.edu
ADD COMMENTlink written 11.0 years ago by Jenny Drnevich2.2k
Hi Jenny, It seems that the piece that produces windows binaries of the annotation packages has been broken. We should be able to push new versions first thing on Monday. If you have the ability to build windows packages, you could do that directly from the source package. sorry about that Robert Jenny Drnevich wrote: >> Yes, this is not as desired. But can you please try updating the GO >> package and see if this remains to be an issue :-) >> >> BTW, I believe this hasn't changed since your last update so I will >> recommend how to update: >> >> library(Biobase) >> update.packages(repos=biocReposList()) >> >> + seth > > As of 2 minutes ago, these were the only packages that it updated... > > package 'affyio' successfully unpacked and MD5 sums checked > package 'annaffy' successfully unpacked and MD5 sums checked > package 'annotate' successfully unpacked and MD5 sums checked > package 'AnnotationDbi' successfully unpacked and MD5 sums checked > package 'biomaRt' successfully unpacked and MD5 sums checked > package 'Category' successfully unpacked and MD5 sums checked > package 'GOstats' successfully unpacked and MD5 sums checked > package 'graph' successfully unpacked and MD5 sums checked > package 'preprocessCore' successfully unpacked and MD5 sums checked > > ... and I'm still having the same problem. I also tried using > biocLite("GO"), but it downloaded the same version I already had: > 1.17.0. If there's a newer version, it's not available as a Windows > binary. BTW, there is no package "GO" on the BioC website software > listings for either BioC 2.0 or BioC 2.1... > > Thanks, > Jenny > > > >> -- >> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >> BioC: http://bioconductor.org/ >> Blog: http://userprimary.net/user/ > > 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 uiuc.edu > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD REPLYlink written 11.0 years ago by rgentleman5.5k
And there is a much newer source version on the website here: http://www.bioconductor.org/packages/2.1/data/annotation/html/GO.html Best, Jim Robert Gentleman wrote: > Hi Jenny, > It seems that the piece that produces windows binaries of the > annotation packages has been broken. We should be able to push new > versions first thing on Monday. If you have the ability to build > windows packages, you could do that directly from the source package. > > sorry about that > Robert > > > Jenny Drnevich wrote: >>> Yes, this is not as desired. But can you please try updating the GO >>> package and see if this remains to be an issue :-) >>> >>> BTW, I believe this hasn't changed since your last update so I will >>> recommend how to update: >>> >>> library(Biobase) >>> update.packages(repos=biocReposList()) >>> >>> + seth >> As of 2 minutes ago, these were the only packages that it updated... >> >> package 'affyio' successfully unpacked and MD5 sums checked >> package 'annaffy' successfully unpacked and MD5 sums checked >> package 'annotate' successfully unpacked and MD5 sums checked >> package 'AnnotationDbi' successfully unpacked and MD5 sums checked >> package 'biomaRt' successfully unpacked and MD5 sums checked >> package 'Category' successfully unpacked and MD5 sums checked >> package 'GOstats' successfully unpacked and MD5 sums checked >> package 'graph' successfully unpacked and MD5 sums checked >> package 'preprocessCore' successfully unpacked and MD5 sums checked >> >> ... and I'm still having the same problem. I also tried using >> biocLite("GO"), but it downloaded the same version I already had: >> 1.17.0. If there's a newer version, it's not available as a Windows >> binary. BTW, there is no package "GO" on the BioC website software >> listings for either BioC 2.0 or BioC 2.1... >> >> Thanks, >> Jenny >> >> >> >>> -- >>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >>> BioC: http://bioconductor.org/ >>> Blog: http://userprimary.net/user/ >> 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 uiuc.edu >> >> _______________________________________________ >> 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 Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD REPLYlink written 11.0 years ago by James W. MacDonald47k
Well, it's good to know that I'm not a _complete_ idiot :) I didn't realize GO was an annotation/metadata package and not a software package, which is why I couldn't find it on the website. I was able to build from source for the newest versions of GO and GO.db, and the problem with invalid GO terms went away... but then I also built the newest version of the ath1121501 annotation package, and then calling hyperGTest() lead to the following error: Error in getUniverseHelper(probes, datPkg, entrezIds) : No Entrez Gene ids left in universe ARRRGHH! Anyway, I think I'll wait until Tuesday (I'm off on Monday!!) when the windows binaries are hopefully available, update all my packages again, and then see what happens... Thanks for all your help, Jenny At 01:36 PM 9/14/2007, Robert Gentleman wrote: >Hi Jenny, > It seems that the piece that produces windows binaries of the > annotation packages has been broken. We should be able to push new > versions first thing on Monday. If you have the ability to build > windows packages, you could do that directly from the source package. > > sorry about that > Robert > > >Jenny Drnevich wrote: >>>Yes, this is not as desired. But can you please try updating the GO >>>package and see if this remains to be an issue :-) >>> >>>BTW, I believe this hasn't changed since your last update so I will >>>recommend how to update: >>> >>>library(Biobase) >>>update.packages(repos=biocReposList()) >>> >>>+ seth >>As of 2 minutes ago, these were the only packages that it updated... >>package 'affyio' successfully unpacked and MD5 sums checked >>package 'annaffy' successfully unpacked and MD5 sums checked >>package 'annotate' successfully unpacked and MD5 sums checked >>package 'AnnotationDbi' successfully unpacked and MD5 sums checked >>package 'biomaRt' successfully unpacked and MD5 sums checked >>package 'Category' successfully unpacked and MD5 sums checked >>package 'GOstats' successfully unpacked and MD5 sums checked >>package 'graph' successfully unpacked and MD5 sums checked >>package 'preprocessCore' successfully unpacked and MD5 sums checked >>... and I'm still having the same problem. I also tried using >>biocLite("GO"), but it downloaded the same version I already had: >>1.17.0. If there's a newer version, it's not available as a >>Windows binary. BTW, there is no package "GO" on the BioC website >>software listings for either BioC 2.0 or BioC 2.1... >>Thanks, >>Jenny >> >> >>>-- >>>Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >>>BioC: http://bioconductor.org/ >>>Blog: http://userprimary.net/user/ >>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 uiuc.edu >>_______________________________________________ >>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 > >-- >Robert Gentleman, PhD >Program in Computational Biology >Division of Public Health Sciences >Fred Hutchinson Cancer Research Center >1100 Fairview Ave. N, M2-B876 >PO Box 19024 >Seattle, Washington 98109-1024 >206-667-7700 >rgentlem at fhcrc.org 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 uiuc.edu
ADD REPLYlink written 11.0 years ago by Jenny Drnevich2.2k
Hi Jenny, We've just updated many of our metadata packages and we're now providing all the Windows binaries (Mac OS X binaries will come later). Go here for the list of what we have in store http://bioconductor.org/packages/2.1/data/annotation/ and install with biocLite() or update with: > source("http://bioconductor.org/biocLite.R") > update.packages(rep=biocinstallRepos(), ask=FALSE) Let us know if this solves your problem. Cheers, H. Jenny Drnevich wrote: > Well, it's good to know that I'm not a _complete_ idiot :) I didn't > realize GO was an annotation/metadata package and not a software > package, which is why I couldn't find it on the website. I was able > to build from source for the newest versions of GO and GO.db, and the > problem with invalid GO terms went away... but then I also built the > newest version of the ath1121501 annotation package, and then calling > hyperGTest() lead to the following error: > > Error in getUniverseHelper(probes, datPkg, entrezIds) : > No Entrez Gene ids left in universe > > > ARRRGHH! Anyway, I think I'll wait until Tuesday (I'm off on > Monday!!) when the windows binaries are hopefully available, update > all my packages again, and then see what happens... > > Thanks for all your help, > Jenny > > At 01:36 PM 9/14/2007, Robert Gentleman wrote: >> Hi Jenny, >> It seems that the piece that produces windows binaries of the >> annotation packages has been broken. We should be able to push new >> versions first thing on Monday. If you have the ability to build >> windows packages, you could do that directly from the source package. >> >> sorry about that >> Robert >> >> >> Jenny Drnevich wrote: >>>> Yes, this is not as desired. But can you please try updating the GO >>>> package and see if this remains to be an issue :-) >>>> >>>> BTW, I believe this hasn't changed since your last update so I will >>>> recommend how to update: >>>> >>>> library(Biobase) >>>> update.packages(repos=biocReposList()) >>>> >>>> + seth >>> As of 2 minutes ago, these were the only packages that it updated... >>> package 'affyio' successfully unpacked and MD5 sums checked >>> package 'annaffy' successfully unpacked and MD5 sums checked >>> package 'annotate' successfully unpacked and MD5 sums checked >>> package 'AnnotationDbi' successfully unpacked and MD5 sums checked >>> package 'biomaRt' successfully unpacked and MD5 sums checked >>> package 'Category' successfully unpacked and MD5 sums checked >>> package 'GOstats' successfully unpacked and MD5 sums checked >>> package 'graph' successfully unpacked and MD5 sums checked >>> package 'preprocessCore' successfully unpacked and MD5 sums checked >>> ... and I'm still having the same problem. I also tried using >>> biocLite("GO"), but it downloaded the same version I already had: >>> 1.17.0. If there's a newer version, it's not available as a >>> Windows binary. BTW, there is no package "GO" on the BioC website >>> software listings for either BioC 2.0 or BioC 2.1... >>> Thanks, >>> Jenny >>> >>> >>>> -- >>>> Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center >>>> BioC: http://bioconductor.org/ >>>> Blog: http://userprimary.net/user/ >>> 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 uiuc.edu >>> _______________________________________________ >>> 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 >> -- >> Robert Gentleman, PhD >> Program in Computational Biology >> Division of Public Health Sciences >> Fred Hutchinson Cancer Research Center >> 1100 Fairview Ave. N, M2-B876 >> PO Box 19024 >> Seattle, Washington 98109-1024 >> 206-667-7700 >> rgentlem at fhcrc.org > > 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 uiuc.edu > > _______________________________________________ > 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 REPLYlink written 11.0 years ago by Hervé Pagès ♦♦ 13k
Hi Herve, Thanks for letting me know the new Windows binaries were available. However, I traced the problem to the new annotation package for ath1121501 - it is USELESS for GOstats testing!! Arabidopsis doesn't use EntrezIDs, but instead uses AGI locus identifier, given in the ath1121501ACCNUM environment. This environment used to give unique IDs for almost all probe sets, but now all of the listings are either "multiple" or NA: > probes <- ls(ath1121501ACCNUM) > probes[1:10] [1] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" [6] "244906_at" "244907_at" "244908_at" "244909_at" "244910_s_at" > length(probes) [1] 22810 > locusList <- unique(unlist(mget(probes, ath1121501ACCNUM))) > length(locusList) [1] 2 > locusList [1] "multiple" NA I realize this is probably came from the Arabidopsis database used to create the annotation package, but is there any way to "fix" this, or to put up the older annotation package? The old one had a few hundred "multiple" entries, but I figured it wouldn't matter that much to throw them out. Any other ideas for ways around this problem? Thanks, Jenny > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-28 r42679) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets [8] methods base other attached packages: [1] limma_2.11.13 ath1121501_1.99.10 GOstats_2.3.17 [4] Category_2.3.39 genefilter_1.15.11 survival_2.32 [7] RBGL_1.13.6 annotate_1.15.11 xtable_1.5-1 [10] GO.db_1.99.3 AnnotationDbi_0.99.1 RSQLite_0.6-2 [13] DBI_0.2-3 graph_1.15.20 Biobase_1.15.34 loaded via a namespace (and not attached): [1] cluster_1.11.7 simpleaffy_2.13.01 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 uiuc.edu
ADD REPLYlink written 11.0 years ago by Jenny Drnevich2.2k
Hi Jenny, We will have a look and see if something obvious has gone wrong... any arabadopsis experts that might know something more should feel free to venture an opinion here... Jenny Drnevich wrote: > Hi Herve, > > Thanks for letting me know the new Windows binaries were available. > However, I traced the problem to the new annotation package for > ath1121501 - it is USELESS for GOstats testing!! Arabidopsis doesn't use > EntrezIDs, but instead uses AGI locus identifier, given in the > ath1121501ACCNUM environment. This environment used to give unique IDs > for almost all probe sets, but now all of the listings are either > "multiple" or NA: > > > probes <- ls(ath1121501ACCNUM) > > probes[1:10] > [1] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" > [6] "244906_at" "244907_at" "244908_at" "244909_at" "244910_s_at" > > length(probes) > [1] 22810 > > locusList <- unique(unlist(mget(probes, ath1121501ACCNUM))) > > length(locusList) > [1] 2 > > locusList > [1] "multiple" NA > > > I realize this is probably came from the Arabidopsis database used to > create the annotation package, but is there any way to "fix" this, or to > put up the older annotation package? The old one had a few hundred > "multiple" entries, but I figured it wouldn't matter that much to throw > them out. Any other ideas for ways around this problem? > > Thanks, > Jenny > > > sessionInfo() > R version 2.6.0 Under development (unstable) (2007-08-28 r42679) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] limma_2.11.13 ath1121501_1.99.10 GOstats_2.3.17 > [4] Category_2.3.39 genefilter_1.15.11 survival_2.32 > [7] RBGL_1.13.6 annotate_1.15.11 xtable_1.5-1 > [10] GO.db_1.99.3 AnnotationDbi_0.99.1 RSQLite_0.6-2 > [13] DBI_0.2-3 graph_1.15.20 Biobase_1.15.34 > > loaded via a namespace (and not attached): > [1] cluster_1.11.7 simpleaffy_2.13.01 > > > > > > 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 uiuc.edu > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
ADD REPLYlink written 11.0 years ago by rgentleman5.5k
Hi Jenny, Jenny Drnevich wrote: > Hi Herve, > > Thanks for letting me know the new Windows binaries were available. > However, I traced the problem to the new annotation package for > ath1121501 - it is USELESS for GOstats testing!! Arabidopsis doesn't use > EntrezIDs, but instead uses AGI locus identifier, given in the > ath1121501ACCNUM environment. This environment used to give unique IDs > for almost all probe sets, but now all of the listings are either > "multiple" or NA: > >> probes <- ls(ath1121501ACCNUM) >> probes[1:10] > [1] "244901_at" "244902_at" "244903_at" "244904_at" "244905_at" > [6] "244906_at" "244907_at" "244908_at" "244909_at" "244910_s_at" >> length(probes) > [1] 22810 >> locusList <- unique(unlist(mget(probes, ath1121501ACCNUM))) >> length(locusList) > [1] 2 >> locusList > [1] "multiple" NA > > > I realize this is probably came from the Arabidopsis database used to > create the annotation package, but is there any way to "fix" this, or to > put up the older annotation package? The old one had a few hundred > "multiple" entries, but I figured it wouldn't matter that much to throw > them out. Any other ideas for ways around this problem? Thanks for reporting this! The ath1121501ACCNUM map is clearly broken and I will investigate this. Note that there is a simple work around (for now). Here it is. The ath1121501ACCNUM map is in fact derived from the ath1121501MULTIHIT: this one is the original mapping between probes and AGI locus identifiers. But given that this mapping is many-to-many (hence the name "MULTIHIT") some time ago someone has decided to also provide the ath1121501ACCNUM map that would be the same mapping except for the probes that hit nultiple AGI locus ids: in ath1121501ACCNUM those probes would be mapped to the string "multiple". I've checked the ath1121501MULTIHIT map and it looks OK: > tt <- unlist(eapply(ath1121501MULTIHIT, length)) > table(tt) tt 1 2 3 4 5 6 7 8 9 10 12 14 16 21731 945 62 32 14 10 4 4 1 1 1 3 1 17 1 > tt[tt==17] 266769_s_at 17 > ath1121501MULTIHIT[["266769_s_at"]] [1] "AT1G12935" "AT1G18930" "AT2G03080" "AT2G04130" "AT2G04140" "AT3G29440" [7] "AT3G42883" "AT3G44390" "AT3G47165" "AT3G50490" "AT4G12426" "AT4G17820" [13] "AT4G20180" "AT5G26590" "AT5G28466" "AT5G33315" "AT5G56605" You can compute the ath1121501ACCNUM yourself with: > ath1121501ACCNUM <- eapply(ath1121501MULTIHIT, function(ids) if (length(ids) > 1) "multiple" else ids) Let me know if you find any other problem. Thanks! H. > > Thanks, > Jenny > >> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-08-28 r42679) > i386-pc-mingw32 > > locale: > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > States.1252;LC_MONETARY=English_United > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > attached base packages: > [1] splines tools stats graphics grDevices utils datasets > [8] methods base > > other attached packages: > [1] limma_2.11.13 ath1121501_1.99.10 GOstats_2.3.17 > [4] Category_2.3.39 genefilter_1.15.11 survival_2.32 > [7] RBGL_1.13.6 annotate_1.15.11 xtable_1.5-1 > [10] GO.db_1.99.3 AnnotationDbi_0.99.1 RSQLite_0.6-2 > [13] DBI_0.2-3 graph_1.15.20 Biobase_1.15.34 > > loaded via a namespace (and not attached): > [1] cluster_1.11.7 simpleaffy_2.13.01 > > > > > > 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 uiuc.edu
ADD REPLYlink written 11.0 years ago by Hervé Pagès ♦♦ 13k
Hi Herve, Thanks for looking into this. Unfortunately, your fix didn't quite work: >You can compute the ath1121501ACCNUM yourself with: > > > ath1121501ACCNUM <- eapply(ath1121501MULTIHIT, > function(ids) if (length(ids) > 1) > "multiple" else ids) This changes ath1121501ACCNUM from an environment to a list, and to use hyperGTest(), it needs to be an environment. I know very little about environments, and the simple as.environment() didn't work, so I don't know how to fix it. Thanks, Jenny >Let me know if you find any other problem. > >Thanks! >H. > > > > > > Thanks, > > Jenny > > > >> sessionInfo() > > R version 2.6.0 Under development (unstable) (2007-08-28 r42679) > > i386-pc-mingw32 > > > > locale: > > LC_COLLATE=English_United States.1252;LC_CTYPE=English_United > > States.1252;LC_MONETARY=English_United > > States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 > > > > attached base packages: > > [1] splines tools stats graphics grDevices utils datasets > > [8] methods base > > > > other attached packages: > > [1] limma_2.11.13 ath1121501_1.99.10 GOstats_2.3.17 > > [4] Category_2.3.39 genefilter_1.15.11 survival_2.32 > > [7] RBGL_1.13.6 annotate_1.15.11 xtable_1.5-1 > > [10] GO.db_1.99.3 AnnotationDbi_0.99.1 RSQLite_0.6-2 > > [13] DBI_0.2-3 graph_1.15.20 Biobase_1.15.34 > > > > loaded via a namespace (and not attached): > > [1] cluster_1.11.7 simpleaffy_2.13.01 > > > > > > > > > > > > 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 uiuc.edu
ADD REPLYlink written 11.0 years ago by Jenny Drnevich2.2k
Hi Jenny, You want multiassign() in Biobase. Something like this should do the trick: tmp <- eapply(ath1121501MULTIHIT, function(ids) if(length(ids) >1) "multiple" else ids) ath112150ACCNUM <- new.env(hash=TRUE, parent=.GlobalEnv) multiassign(tmp, envir=ath112150ACCNUM) Best, Jim Jenny Drnevich wrote: > Hi Herve, > > Thanks for looking into this. Unfortunately, your fix didn't quite work: > > >> You can compute the ath1121501ACCNUM yourself with: >> >>> ath1121501ACCNUM <- eapply(ath1121501MULTIHIT, >> function(ids) if (length(ids) > 1) >> "multiple" else ids) > > This changes ath1121501ACCNUM from an environment to a list, and to > use hyperGTest(), it needs to be an environment. I know very little > about environments, and the simple as.environment() didn't work, so I > don't know how to fix it. > > Thanks, > Jenny > > > >> Let me know if you find any other problem. >> >> Thanks! >> H. >> >> >>> Thanks, >>> Jenny >>> >>>> sessionInfo() >>> R version 2.6.0 Under development (unstable) (2007-08-28 r42679) >>> i386-pc-mingw32 >>> >>> locale: >>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>> States.1252;LC_MONETARY=English_United >>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>> >>> attached base packages: >>> [1] splines tools stats graphics grDevices utils datasets >>> [8] methods base >>> >>> other attached packages: >>> [1] limma_2.11.13 ath1121501_1.99.10 GOstats_2.3.17 >>> [4] Category_2.3.39 genefilter_1.15.11 survival_2.32 >>> [7] RBGL_1.13.6 annotate_1.15.11 xtable_1.5-1 >>> [10] GO.db_1.99.3 AnnotationDbi_0.99.1 RSQLite_0.6-2 >>> [13] DBI_0.2-3 graph_1.15.20 Biobase_1.15.34 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.7 simpleaffy_2.13.01 >>> >>> >>> >>> >>> >>> 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 uiuc.edu > > _______________________________________________ > 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, MS Biostatistician UMCCC cDNA and Affymetrix Core University of Michigan 1500 E Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623
ADD REPLYlink written 11.0 years ago by James W. MacDonald47k
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