[BioC] Error in setQCEnvironment(cdfn)

James W. MacDonald jmacdon at uw.edu
Tue Sep 4 17:58:19 CEST 2012

Hi Suparna,

On 9/4/2012 11:35 AM, suparna mitra wrote:
> Hello group,
>   I am new in bioconductor and trying use it for my Affymetrix microarray
> data.
> Genechip HuGene-1_0-st-v1.

The simpleaffy package isn't really designed for this array. A 
significant portion of the QC measures are based on comparisons between 
the PM and MM probes, and the newer generation of arrays from Affy no 
longer have MM probes.



> I have normalized my data using rma. Then when I trying to see the quality
> I found following error. Can anybody help me with this please.
> Thanks a lot in advance :)
> Best wishes,
> Suparna.
>> library(affy)
>> library(simpleaffy)
> Loading required package: genefilter
> Loading required package: gcrma
> Attaching package: 'simpleaffy'
> The following object(s) are masked _by_ '.GlobalEnv':
>      getBioC
>> library("hugene10stv1cdf")
>> aqc<-qc(InVivodata)
> Error in setQCEnvironment(cdfn) :
>    Could not find array definition file ' hugene10stv1cdf.qcdef '.
> Simpleaffy does not know the QC parameters for this array type.
> See the package vignette for details about how to specify QC parameters
> manually.
> 	[[alternative HTML version deleted]]
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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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