[BioC] Prokaryotic_Rhodobacter capsulatus GEP

[Martin Morgan]

Mark Robinson <mrobinson at wehi.EDU.AU> writes:

> 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?

The Bioconductor makecdfenv package makes cdf environments from cdf
files.

Martin

> 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
>
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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