[BioC] limma for R 2.6

[Martin Morgan]

Hi Tiandao

There are likely to be minor changes prior to the release, so I would
recommend updating packages (using the same procedure) shortly after
when the release is announced.

Martin


Tiandao Li <Tiandao.Li at usm.edu> writes:

> Hi Martin,
>
> I update BioC as you suggested, the problem is solved. One more question, 
> should I update BioC again after this Friday?
>
> Thanks,
>
> Tiandao
>
>> sessionInfo()
> R version 2.6.0 (2007-10-03) 
> i486-pc-linux-gnu 
>
> locale:
> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] limma_2.12.0
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-15
>
>
>
>
> On Thu, 4 Oct 2007, Martin Morgan wrote:
>
> Yes, your limma (2.10.5) is suitable for R 2.5 or 2.5.1 but you are
> using R 2.6.
>
> You will need to update your packages, as outlined in the original
> response. Here's what my R 2.6 looks like after following those
> directions and then, in a new session, library(limma). Note the
> limma version number.
>
>> sessionInfo()
> R version 2.6.0 Patched (2007-10-04 r43081) 
> x86_64-unknown-linux-gnu 
>
> locale:
> LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY=en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] limma_2.12.0
>
> loaded via a namespace (and not attached):
> [1] rcompgen_0.1-15
>
> Maritn
>
> Tiandao Li <Tiandao.Li at usm.edu> writes:
>
>> Hi Martin,
>>
>>> sessionInfo()
>> R version 2.6.0 (2007-10-03) 
>> i486-pc-linux-gnu 
>>
>> locale:
>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats     graphics  grDevices utils     datasets  methods   base     
>>
>> other attached packages:
>> [1] MASS_7.2-36   statmod_1.3.1 limma_2.10.5 
>>
>> loaded via a namespace (and not attached):
>> [1] rcompgen_0.1-15
>>
>>
>>
>> On Thu, 4 Oct 2007, Martin Morgan wrote:
>>
>> Hi Tiandao --
>>
>> I'm guess that you updated R but not your Bioconductor packages --
>> please provide sessionInfo() in all posts! There are instructions for
>> updating packages on the Bioconductor web site
>>
>> http://www.bioconductor.org/docs/install-howto.html
>>
>> at the bottom of the page:
>>
>> source("http://bioconductor.org/biocLite.R")
>> biocLite("Biobase")
>> library(Biobase)
>> repos <- biocReposList()
>> update.packages(repos=repos, ask=FALSE)
>>
>> You should be careful to do this in an R session that does not hae any
>> packages attached, because attached packages cannot be updated.
>>
>> The bioconductor release is being finalized, so you might find it
>> helpful to run update.packages again after the release.
>>
>> Please let the list know if this solves your problem. 
>>
>> Martin
>>
>> Tiandao Li <Tiandao.Li at usm.edu> writes:
>>
>>> Hello,
>>>
>>> I upgraded R from 2.5.1 to 2.6 on Ubuntu this morning. However, when I ran 
>>> normalization using printtiploess, it showed the following error.
>>>
>>>> MA2 <- normalizeWithinArrays(RG, method="printtiploess")
>>> Error in .C("lowess", x = as.double(xobs[o]), as.double(yobs[o]), nobs,  :
>>>    C symbol name "lowess" not in DLL for package "base"
>>>
>>> However, no error for the next one.
>>>
>>>> MA3 <- normalizeWithinArrays(RG, method="printtiploess", weights=weight)
>>>
>>> Any suggests are welcome!
>>>
>>> Tiandao
>>>
>>> _______________________________________________
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>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
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>>
>> -- 
>> Martin Morgan
>> Bioconductor / Computational Biology
>> http://bioconductor.org
>>
>> _______________________________________________
>> Bioconductor mailing list
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>
> -- 
> Martin Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org

-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org