[BioC] downloading problems

Marcus Davy MDavy at hortresearch.co.nz
Wed Nov 24 01:38:09 CET 2004

Works fine for me on an OS X machine running Panther 10.3.5 freshly installed with R-2.0.1
and the getBioC() script.

>  library(Biobase)
>  library(golubEsets)
> find("exprs")
[1] "package:Biobase"
>  library(golubEsets)
> hist(exprs(golubMerge))
> exprs(golubMerge)
                              [,1]   [,2]   [,3]  [,4]   [,5]   [,6]
AFFX-BioB-5_at                -342    -87     22  -243   -130   -256
AFFX-BioB-M_at                -200   -248   -153  -218   -177   -249
AFFX-BioB-3_at                  41    262     17  -163    -28   -410
AFFX-BioC-5_at                 328    295    276   182    266     24
AFFX-BioC-3_at                -224   -226   -211  -289   -170   -535

Since it looks like you cannot even access the exprs object in the Biobase package (does this still exist when quiting R and re-running it?), I would suggest that something is badly wrong with your install. Easiest to probably reinstall R as administrator and then install Bioconductor using the getBioC() script. As in my previous email on OS X installation I would install the binary XML package from the pull down menus before installing Bioconductor using getBioC.


>>> Katie Roberts <katier23 at stanford.edu> 24/11/2004 6:24:32 AM >>>


I think the problem is in the downloading of the contents of the packages,
when I enter library() the packages appear to be there, but then I can't
access them.

> library(Biobase)
Loading required package: tools
> library()
> library(golubEsets)
> hist(exprs(golubMerge))
Error in hist(exprs(golubMerge)) : couldn't find function "exprs"
> exprs(golubMerge)
Error: couldn't find function "exprs"

Data set 'geneData' not found in: data(geneData)
> data(geneCov)
Warning message:
Data set 'geneCov' not found in: data(geneCov)

I'm using the most recent getBioC() from the website, and have tried
downloading everything at once, as well as packages separately. I'm using a
Mac OSX 10.3 and have also tried turning off the firewall prior to
downloading, but that hasn't seemed to make a difference.


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