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Question: older version of org.Hs.eg.db
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4.4 years ago by
Guest User12k
Guest User12k wrote:
Hi all, Hopefully this is the right mailinglist for my problem: I'm searching for an older version of the data-package org.Hs.eg.db. More exactly: a version of september 2010 I compared a programms output I got in R with the output of GeneTrail (an online Tool). GeneTrail uses a database version from 2010-09-02. I'm getting different outputs and was wondering if I made a mistake in my programm or if it's just because of the different versions of the data. To exclude the 2nd point I need that older version. I searched for it on the Bioconductor page but couldn't find it. Thanking you for your help in anticipation. 1frcn -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C [5] LC_TIME=German_Germany.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base -- Sent via the guest posting facility at bioconductor.org.
ADD COMMENTlink modified 4.4 years ago by Dan Du210 • written 4.4 years ago by Guest User12k
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gravatar for Dan Du
4.4 years ago by
Dan Du210
Germany
Dan Du210 wrote:
Hi 1frcn, this one should be close enough, http://bioconductor.org/packages/2.7/data/annotation/html/org.Hs.eg.db .html with a time stamp "Packaged: 2010-10-04 18:33:30 UTC; mcarlson", while there is no guarantee that this will match to the one GeneTrail was using. Best, dan On Wed, 2014-04-16 at 04:12 -0700, 1frcn [guest] wrote: > Hi all, > > Hopefully this is the right mailinglist for my problem: > I'm searching for an older version of the data-package org.Hs.eg.db. More exactly: a version of september 2010 > > I compared a programms output I got in R with the output of GeneTrail (an online Tool). GeneTrail uses a database version from 2010-09-02. I'm getting different outputs and was wondering if I made a mistake in my programm or if it's just because of the different versions of the data. To exclude the 2nd point I need that older version. I searched for it on the Bioconductor page but couldn't find it. > > Thanking you for your help in anticipation. > 1frcn > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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
ADD COMMENTlink written 4.4 years ago by Dan Du210
Hi dan, thanks a lot for your answer! This would have been perfekt - unfortunally it didn't help cause we're using our own R-packages and they aren't compatible with older R versions and the older version of org.Hs.eg.db isn't working with the new R version. -.- So I guess I've to check my programm again and see if I can find a mistake... Thanks again, 1frcn Gesendet: Mittwoch, 16. April 2014 um 13:42 Uhr Von: "Dan Du" <tooyoung at="" gmail.com=""> An: "1frcn [guest]" <guest at="" bioconductor.org=""> Cc: bioconductor at r-project.org, 1frcn at ist-einmalig.de Betreff: Re: [BioC] older version of org.Hs.eg.db Hi 1frcn, this one should be close enough, [1]http://bioconductor.org/packages/2.7/data/annotation/html/org.Hs .eg.db.ht ml with a time stamp "Packaged: 2010-10-04 18:33:30 UTC; mcarlson", while there is no guarantee that this will match to the one GeneTrail was using. Best, dan On Wed, 2014-04-16 at 04:12 -0700, 1frcn [guest] wrote: > Hi all, > > Hopefully this is the right mailinglist for my problem: > I'm searching for an older version of the data-package org.Hs.eg.db. More exactly: a version of september 2010 > > I compared a programms output I got in R with the output of GeneTrail (an online Tool). GeneTrail uses a database version from 2010-09-02. I'm getting different outputs and was wondering if I made a mistake in my programm or if it's just because of the different versions of the data. To exclude the 2nd point I need that older version. I searched for it on the Bioconductor page but couldn't find it. > > Thanking you for your help in anticipation. > 1frcn > > -- output of sessionInfo(): > > R version 3.0.2 (2013-09-25) > Platform: x86_64-w64-mingw32/x64 (64-bit) > > locale: > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > [5] LC_TIME=German_Germany.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > [2]https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: [3]http://news.gmane.org/gmane.science.biology.informatics.conductor References 1. http://bioconductor.org/packages/2.7/data/annotation/html/org.Hs .eg.db.html 2. https://stat.ethz.ch/mailman/listinfo/bioconductor 3. http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD REPLYlink written 4.4 years ago by 1frcn20
Hi 1frcn, Bioconductor packages are not intended to be cross-compatible with all other versions. So if you really need to use an annotation package from 2010, then you will need to also be running the older software that it was test with/against. You can do this by simply installing the appropriate version of R (in this case it would be R version 2.12 that was run with Bioconductor 2.7) an then using biocLite() (as described here): http://bioconductor.org/install/ Once you have set up the packages using biocLite() in this way, you should automatically have the old annotations installed alongside their matching old software. Marc On 04/16/2014 05:19 AM, 1frcn at ist-einmalig.de wrote: > Hi dan, > thanks a lot for your answer! This would have been perfekt - unfortunally it > didn't help cause we're using our own R-packages and they aren't compatible > with older R versions and the older version of org.Hs.eg.db isn't working > with the new R version. -.- > So I guess I've to check my programm again and see if I can find a > mistake... > Thanks again, > 1frcn > > Gesendet: Mittwoch, 16. April 2014 um 13:42 Uhr > Von: "Dan Du" <tooyoung at="" gmail.com=""> > An: "1frcn [guest]" <guest at="" bioconductor.org=""> > Cc: bioconductor at r-project.org, 1frcn at ist-einmalig.de > Betreff: Re: [BioC] older version of org.Hs.eg.db > Hi 1frcn, > this one should be close enough, > [1]http://bioconductor.org/packages/2.7/data/annotation/html/org .Hs.eg.db.ht > ml > with a time stamp "Packaged: 2010-10-04 18:33:30 UTC; mcarlson", > while there is no guarantee that this will match to the one GeneTrail > was using. > Best, > dan > On Wed, 2014-04-16 at 04:12 -0700, 1frcn [guest] wrote: > > Hi all, > > > > Hopefully this is the right mailinglist for my problem: > > I'm searching for an older version of the data-package org.Hs.eg.db. More > exactly: a version of september 2010 > > > > I compared a programms output I got in R with the output of GeneTrail (an > online Tool). GeneTrail uses a database version from 2010-09-02. I'm getting > different outputs and was wondering if I made a mistake in my programm or if > it's just because of the different versions of the data. To exclude the 2nd > point I need that older version. I searched for it on the Bioconductor page > but couldn't find it. > > > > Thanking you for your help in anticipation. > > 1frcn > > > > -- output of sessionInfo(): > > > > R version 3.0.2 (2013-09-25) > > Platform: x86_64-w64-mingw32/x64 (64-bit) > > > > locale: > > [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252 > > [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C > > [5] LC_TIME=German_Germany.1252 > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > > > -- > > Sent via the guest posting facility at bioconductor.org. > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at r-project.org > > [2]https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > [3]http://news.gmane.org/gmane.science.biology.informatics.conductor > > References > > 1. http://bioconductor.org/packages/2.7/data/annotation/html/org .Hs.eg.db.html > 2. https://stat.ethz.ch/mailman/listinfo/bioconductor > 3. http://news.gmane.org/gmane.science.biology.informatics.conductor > _______________________________________________ > 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
ADD REPLYlink written 4.4 years ago by Marc Carlson7.2k
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