[BioC] Specifying a local CDF file for use with fitPLM or others

[James W. MacDonald]

Hi Vincent,

Vincent Davis wrote:
> I am very new to R and bioconductor, I assume this is obscure but easy. I
> have CEL fils from a custom Affymetrix array. I also have a CDF.
> I have imported the cel files using
>     abatch <-
> ReadAffy(celfile.path='/Users/vmd/Dropbox/dna/data/Raw_Data_CEL_Zip/Type_1')
> then trying to use fitPLM()
>     Pset <- fitPLM(abatch)
> I get this error:
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.10
> Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain Tgondiia520372
> Library - package tgondiia520372cdf not installed
> Bioconductor - tgondiia520372cdf not available
> 
> I have the CDF file but am unsure how to instruct fitPLM to reference it?

You need to use the makecdfenv package. There is a vignette that comes 
with the package that shows how to create and install the package.

Best,

Jim


> 
> 
>   *Vincent Davis
> 720-301-3003 *
> vincent at vincentdavis.net
>  my blog <http://vincentdavis.net> |
> LinkedIn<http://www.linkedin.com/in/vincentdavis>
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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