[BioC] Error in getCdfInfo(object) when using QCReport

[James W. MacDonald]

Hi Xingmei,

Xingmei Wang wrote:
> My code is as following:
>> setwd("G:/XWang/microarray_phototherapy/CEL file")
>> library(affyQCReport)
> Loading required package: Biobase
> Loading required package: tools
> Welcome to Bioconductor
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> Loading required package: affy
> Loading required package: simpleaffy
> Loading required package: genefilter
> Loading required package: survival
> Loading required package: splines
> Loading required package: gcrma
> Loading required package: matchprobes
> Loading required package: xtable
> Loading required package: affyPLM
> Loading required package: preprocessCore
> Loading required package: RColorBrewer
> Loading required package: geneplotter
> Loading required package: lattice
> Loading required package: annotate
> Loading required package: AnnotationDbi
> KernSmooth 2.22 installed
> Copyright M. P. Wand 1997
>> mydata<-ReadAffy()
>> QCReport(mydata, file="GelfandQC.pdf")
> Error in getCdfInfo(object) : 
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain HuGene-1_0-st-v1
> Library - package hugene10stv1cdf not installed
> Bioconductor - hugene10stv1cdf not available
> Any suggestion would be highly appreciated!

The affyQCReport uses the affy package for doing the analysis. 
Unfortunately, the affy package doesn't support the HuGene chips. To 
analyze these chips you need to use either oligo or xps.

Best,

Jim


> Xingmei
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662