[BioC] no direct or inherited method for function phenoData

[Seth Falcon]

"Lina Hultin-Rosenberg" <Lina.Hultin.Rosenberg at ebc.uu.se> writes:

> Hi Jim!
>
> I installed the packages by using R CMD INSTALL "package name". This is the
> result of sessionInfo:
>
> __________________________________________________________________
>> sessionInfo()
> Version 2.3.1 (2006-06-01)
> i686-pc-linux-gnu
>
> attached base packages:
> [1] "tools"     "methods"   "stats"     "graphics"  "grDevices" "utils"
> [7] "datasets"  "base"
>
> other attached packages:
>     affy   affyio  Biobase
> 1.10.0  "1.0.0"  "1.8.0"
> _____________________________________________________________________

The Biobase you want is version 1.10.1.  Here is the best way to
install BioC packages (assuming you are connected to the internet):

Start R and then enter:

  source("http://bioconductor.org/biocLite.R")
  biocLite("Biobase")

Note that you can install many packages at once by providing a vector
of package names.  This tool will install required dependencies as
well.  You can also pass it most (all?) of the arguments accepted by
the install.packages function.  This is useful for setting the
installation directory or if you need to alter the download method to
get around a web proxy.

Lastly, you might consider running update.packages in case you have
other such mismatches.  First, upgrade Biobase as shown above, then
do:

library("Biobase")
update.packages(repos=biocReposList())

After all of that, try your examples again and let us know if you
encounter the same problem.

Best,

+ seth