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]]
> >
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> > Bioconductor@r-project.org
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>

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