[BioC] Prokaryotic_Rhodobacter capsulatus GEP

[Mark Robinson]

Hi Dorothy.

In general you can't install packages by copying files to your library  
directory.  And, my guess is that your CDF *file* is not a CDF  
*package*, as required by affy.  Or, is it?

Is your file a text file ... something of the this format?
http://www.affymetrix.com/support/developer/powertools/changelog/gcos-agcc/cdf.html

If it is, you could use 'convertCdf' in the affxparser package, giving  
you a CDF *file*, which you could use within aroma.affymetrix.  There  
also may be a way of converting this into a CDF package, but I don't  
know how.  Anyone else?

If it is not of this format, please let us know what it is.

Mark



On 28/11/2008, at 12:14 PM, dorothyc wrote:

> Hi,
>
> I'm a computational biologist at Genome Sciences Centre, Vancouver,
> BC, Canada.  I'm working on Affymetrix custom bacterial ship,
> Prokaryotic_Rhodobacter capsulatus GEP.
>
> I've encountered some problems with the CDF file.  I've copied the
> rcapex1a520469fcdf directory to /Library/Frameworks/R.framework/
> Versions/2.7/Resources/library.  However, I got an error as follows:
> --------------
>> require(rcapex1a520469fcdf)
> Loading required package: rcapex1a520469fcdf
> Error in library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE,  :
>   'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0?
>
>> raw.data <- ReadAffy()
>> eset <<- rma(raw.data)
> Error in library("rcapex1a520469fcdf", lib.loc = NULL, character.only
> = TRUE) :
>   'rcapex1a520469fcdf' is not a valid package -- installed < 2.0.0?
>
>> library()
> ....
> plier                   Implements the Affymetrix PLIER algorithm
> preprocessCore          A collection of pre-processing functions
> rcapex1a520469fcdf      ** No title available (pre-2.0.0 install?) **
> rpart                   Recursive Partitioning
> ...
> ------------------
> Was the CDF not installed properly?  I was given the cdf file, not the
> tar.gz file; otherwise, I'd have used R CMD INSTALL.
>
> Your feedback is very much appreciated.
>
> Thanks,
> Dorothy
> 	[[alternative HTML version deleted]]
>
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------------------------------
Mark Robinson
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robinson at garvan.org.au
e: mrobinson at wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852