[BioC] Odd warning in simpleaffy, using quality control

[David Westergaard]

Hi Maciej,

The cdf package is installed and working. (I've been preprocessing the
same datafiles using 'affy') I still (almost) the same error:

Attaching package: 'hugene10stv1cdf'

The following object(s) are masked from 'package:hgu133plus2cdf':

    i2xy, xy2i

Error: NAs in foreign function call (arg 1)
In addition: Warning message:
In qc.affy(unnormalised, ...) :
  CDF Environment name ' hgu133plus2cdf ' does not match cdfname '
hugene10stv1cdf '

I might have missunderstood something. Does the qc function in
simpleaffy not recognize cdfName by itself, or do I have to specify
it?

Best,
David


2012/2/27 Maciej Jończyk <mjonczyk at biol.uw.edu.pl>:
> 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
>
>
>
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