[BioC] Error in setQCEnvironment(cdfn)

[James W. MacDonald]

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.

Best,

Jim


>
> 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.
>
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099