[BioC] Odd warning in simpleaffy, using quality control

[Maciej Jończyk]

Hi David,

> I'm trying to run some quality control (qc) on a bunch of raw files
> retrieved from ArrayExpress, using simpleaffy, with the code:
>
> mixture.batch <- ReadAffy()
> mixture.qc <- qc(mixture.batch)
>
> However, when I get to an experiment which has not used the
> "hgu133plus2cdf" platform (In this case, it is experiment
> E-GEOD-33443), I encounter a warning:
>
>
> Error in getCdfInfo(object) :
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain hugene10stv1.r3cdf
> Library - package hugene10stv1.r3cdf not installed
> Bioconductor - hugene10stv1.r3cdf not available
> In addition: Warning message:
> In qc.affy(unnormalised, ...) :
>   CDF Environment name ' hgu133plus2cdf ' does not match cdfname '
> hugene10stv1.r3cdf '

you need appropriate package containing cdf and probe info.

see:
http://www.bioconductor.org/packages/release/data/annotation/

there are hugene10stv1cdf and hugene10stv1probe, maybe it will fit your 
needs.
Alternatively read about makecdf package.

HTH

-- 
Maciej Jonczyk,
Department of Plant Molecular Ecophysiology
Faculty of Biology, University of Warsaw
02-096 Warsaw, Miecznikowa 1
Poland



-- 
This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com