[BioC] limma for R 2.6

[Tiandao Li]

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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