[BioC] limma for R 2.6

[Tiandao Li]

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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>
> -- 
> Martin Morgan
> Bioconductor / Computational Biology
> http://bioconductor.org
>
> _______________________________________________
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> Bioconductor at stat.math.ethz.ch
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-- 
Martin Morgan
Bioconductor / Computational Biology
http://bioconductor.org