[BioC] proper way to handle small changes from different package versions

[Dan Tenenbaum]

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-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]]
>>>
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>>>
>>
>> --
>> 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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