proper way to handle small changes from different package versions
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Juliet Hannah ▴ 360
@juliet-hannah-4531
Last seen 5.6 years ago
United States
All, I had used the lumi package two years ago to analyze Illumina microarray data. I saved the normalized file and have been working with that. I have been asked by GEO to provide a file that has not been preprocessed fully. However, perhaps because of minor changes, the resulting number of probes excluded changes from what I had documented in the past (using the same script). It seems my path forward should be to use an older version of lumi (where can I find this) and try and see if that gives me the same number as before. How can I install this older version? Thanks, Juliet [[alternative HTML version deleted]]
lumi lumi • 1.0k views
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@james-w-macdonald-5106
Last seen 1 day ago
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Hi Juliet, It depends on what version of R you had installed at the time. Two years ago it would have probably been R-2.14.0 or so. You will really need to know which version of R you were using, as the lumi package version is tied to the R version. Anyway, you don't say what OS we are talking about, but you want to go to one of these repositories Linux: http://cran.r-project.org/src/base/R-2/ Windows: http://cran.r-project.org/bin/windows/base/old/ MacOS http://cran.r-project.org/bin/macosx/old/ And install whatever version you think it might have been. After installing, you can then just do source("http://www.bioconductor.org/biocLite.R") biocLite() biocLite("lumi") Best, Jim On 5/31/2013 9:22 AM, Juliet Hannah wrote: > All, > > I had used the lumi package two years ago to analyze Illumina microarray > data. I saved the normalized file and have been working with that. I have > been asked by GEO to provide a file that has not been preprocessed fully. > However, perhaps because of minor changes, the resulting number of probes > excluded changes from what I had documented in the past (using the same > script). > > It seems my path forward should be to use an older version of lumi (where > can I find this) and try and see if that gives me the same number as > before. How can I install this older version? > > Thanks, > > Juliet > > [[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
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Thanks Jim. I always forget the OS. It was Linux. So if I install an older version of R and use biocLite in the usual way, it will install and older version of lumi? Thanks for your help. On Fri, May 31, 2013 at 9:51 AM, James W. MacDonald <jmacdon@uw.edu> wrote: > Hi Juliet, > > It depends on what version of R you had installed at the time. Two years > ago it would have probably been R-2.14.0 or so. You will really need to > know which version of R you were using, as the lumi package version is tied > to the R version. > > Anyway, you don't say what OS we are talking about, but you want to go to > one of these repositories > > Linux: > > http://cran.r-project.org/src/**base/R-2/<http: cran.r-project.org="" src="" base="" r-2=""/> > > Windows: > > http://cran.r-project.org/bin/**windows/base/old/<http: cran.r-proj="" ect.org="" bin="" windows="" base="" old=""/> > > MacOS > > http://cran.r-project.org/bin/**macosx/old/<http: cran.r-project.or="" g="" bin="" macosx="" old=""/> > > And install whatever version you think it might have been. > > After installing, you can then just do > > source("http://www.**bioconductor.org/biocLite.R<http: www.biocondu="" ctor.org="" bioclite.r=""> > ") > biocLite() > biocLite("lumi") > > > Best, > > Jim > > > > > On 5/31/2013 9:22 AM, Juliet Hannah wrote: > >> All, >> >> I had used the lumi package two years ago to analyze Illumina microarray >> data. I saved the normalized file and have been working with that. I have >> been asked by GEO to provide a file that has not been preprocessed fully. >> However, perhaps because of minor changes, the resulting number of probes >> excluded changes from what I had documented in the past (using the same >> script). >> >> It seems my path forward should be to use an older version of lumi (where >> can I find this) and try and see if that gives me the same number as >> before. How can I install this older version? >> >> Thanks, >> >> Juliet >> >> [[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]]
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On Fri, May 31, 2013 at 7:04 AM, Juliet Hannah <juliet.hannah at="" gmail.com=""> wrote: > Thanks Jim. I always forget the OS. It was Linux. So if I install an older > version of R and use biocLite in the > usual way, it will install and older version of lumi? Yes. Do you know what version of lumi you used before? You could find out the appropriate R and BioC version by looking at: http://bioconductor.org/packages/2.12/bioc/html/lumi.html 2.12 is the current release version of Bioconductor. If you scroll to the bottom of the page, you see that lumi is at version 2.12 (coincidentally) for this release. Then replace the 2.12 in the URL with 2.11, and repeat until you see a lumi version number that matches the one you're looking for (it's probably OK if the last segment of the version number, the z in x.y.z, does not match). Then you know the version of _Bioconductor_ you are looking for. To find the version of R you are looking for, go to http://bioconductor.org/help/ And look at the Previous Versions section. The version of R is in parentheses next to the version of Bioconductor. If you install that version of R and run biocLite in the normal way, it will install the appropriate version of lumi. HTH Dan Thanks for your help. > > > On Fri, May 31, 2013 at 9:51 AM, James W. MacDonald <jmacdon at="" uw.edu=""> wrote: > >> Hi Juliet, >> >> It depends on what version of R you had installed at the time. Two years >> ago it would have probably been R-2.14.0 or so. You will really need to >> know which version of R you were using, as the lumi package version is tied >> to the R version. >> >> Anyway, you don't say what OS we are talking about, but you want to go to >> one of these repositories >> >> Linux: >> >> http://cran.r-project.org/src/**base/R-2/<http: cran.r-project.org="" src="" base="" r-2=""/> >> >> Windows: >> >> http://cran.r-project.org/bin/**windows/base/old/<http: cran.r-pro="" ject.org="" bin="" windows="" base="" old=""/> >> >> MacOS >> >> http://cran.r-project.org/bin/**macosx/old/<http: cran.r-project.o="" rg="" bin="" macosx="" old=""/> >> >> And install whatever version you think it might have been. >> >> After installing, you can then just do >> >> source("http://www.**bioconductor.org/biocLite.R<http: www.biocond="" uctor.org="" bioclite.r=""> >> ") >> biocLite() >> biocLite("lumi") >> >> >> Best, >> >> Jim >> >> >> >> >> On 5/31/2013 9:22 AM, Juliet Hannah wrote: >> >>> All, >>> >>> I had used the lumi package two years ago to analyze Illumina microarray >>> data. I saved the normalized file and have been working with that. I have >>> been asked by GEO to provide a file that has not been preprocessed fully. >>> However, perhaps because of minor changes, the resulting number of probes >>> excluded changes from what I had documented in the past (using the same >>> script). >>> >>> It seems my path forward should be to use an older version of lumi (where >>> can I find this) and try and see if that gives me the same number as >>> before. How can I install this older version? >>> >>> Thanks, >>> >>> Juliet >>> >>> [[alternative HTML version deleted]] >>> >>> ______________________________**_________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor<https: stat.="" ethz.ch="" mailman="" listinfo="" bioconductor=""> >>> Search the archives: http://news.gmane.org/gmane.** >>> science.biology.informatics.**conductor<http: news.gmane.org="" gman="" e.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]] > > _______________________________________________ > 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
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Thanks Dan. This is helpful. Unfortunately, I did not record the version I was using. Hopefully, I can track it down with your and Jim's tips. On Fri, May 31, 2013 at 11:49 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote: > On Fri, May 31, 2013 at 7:04 AM, Juliet Hannah <juliet.hannah@gmail.com> > wrote: > > Thanks Jim. I always forget the OS. It was Linux. So if I install an > older > > version of R and use biocLite in the > > usual way, it will install and older version of lumi? > > Yes. Do you know what version of lumi you used before? > > You could find out the appropriate R and BioC version by looking at: > > http://bioconductor.org/packages/2.12/bioc/html/lumi.html > 2.12 is the current release version of Bioconductor. > If you scroll to the bottom of the page, you see that lumi is at > version 2.12 (coincidentally) for this release. > > Then replace the 2.12 in the URL with 2.11, and repeat until you see a > lumi version number that matches the one you're looking for (it's > probably OK if the last segment of the version number, the z in x.y.z, > does not match). > > Then you know the version of _Bioconductor_ you are looking for. > To find the version of R you are looking for, go to > http://bioconductor.org/help/ > > And look at the Previous Versions section. The version of R is in > parentheses next to the version of Bioconductor. If you install that > version of R and run biocLite in the normal way, it will install the > appropriate version of lumi. > > HTH > Dan > > > Thanks for your help. > > > > > > On Fri, May 31, 2013 at 9:51 AM, James W. MacDonald <jmacdon@uw.edu> > wrote: > > > >> Hi Juliet, > >> > >> It depends on what version of R you had installed at the time. Two years > >> ago it would have probably been R-2.14.0 or so. You will really need to > >> know which version of R you were using, as the lumi package version is > tied > >> to the R version. > >> > >> Anyway, you don't say what OS we are talking about, but you want to go > to > >> one of these repositories > >> > >> Linux: > >> > >> http://cran.r-project.org/src/**base/R-2/< > http://cran.r-project.org/src/base/R-2/> > >> > >> Windows: > >> > >> http://cran.r-project.org/bin/**windows/base/old/< > http://cran.r-project.org/bin/windows/base/old/> > >> > >> MacOS > >> > >> http://cran.r-project.org/bin/**macosx/old/< > http://cran.r-project.org/bin/macosx/old/> > >> > >> And install whatever version you think it might have been. > >> > >> After installing, you can then just do > >> > >> source("http://www.**bioconductor.org/biocLite.R< > http://www.bioconductor.org/biocLite.R> > >> ") > >> biocLite() > >> biocLite("lumi") > >> > >> > >> Best, > >> > >> Jim > >> > >> > >> > >> > >> On 5/31/2013 9:22 AM, Juliet Hannah wrote: > >> > >>> All, > >>> > >>> I had used the lumi package two years ago to analyze Illumina > microarray > >>> data. I saved the normalized file and have been working with that. I > have > >>> been asked by GEO to provide a file that has not been preprocessed > fully. > >>> However, perhaps because of minor changes, the resulting number of > probes > >>> excluded changes from what I had documented in the past (using the same > >>> script). > >>> > >>> It seems my path forward should be to use an older version of lumi > (where > >>> can I find this) and try and see if that gives me the same number as > >>> before. How can I install this older version? > >>> > >>> Thanks, > >>> > >>> Juliet > >>> > >>> [[alternative HTML version deleted]] > >>> > >>> ______________________________**_________________ > >>> Bioconductor mailing list > >>> Bioconductor@r-project.org > >>> https://stat.ethz.ch/mailman/**listinfo/bioconductor< > https://stat.ethz.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]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
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