[BioC] Prokaryotic_Rhodobacter capsulatus GEP

[James W. MacDonald]

Looking at the output that the OP has provided implies to me that she 
used the makecdfenv package to create a cdf package, but installed it 
incorrectly.

Dorothy - you did everything correctly up until the last step. You have 
to use R CMD INSTALL to install any package, whether or not it has a 
.tar.gz suffix (which you could make using R CMD build, but this is not 
necessary).

So just move the folder back out onto e.g., your desktop and then install.

Best,

Jim


Martin Morgan wrote:
> 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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> 

-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662