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

[Xingmei Wang]

Thanks a lot Jim for your quick response!

James W. MacDonald wrote:
> 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.
I'm still new in this field, so will need to do some reading on what you 
suggested. Thanks again!
>
> Best,
>
> Jim
>
>
>> Xingmei
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>

-- 
Xingmei wang , MS
Biostatistician

Biostatistics Analysis Center (BAC)
University of Pennsylvania School of Medicine
Center for Clinical Epidemiology and Biostatistics
519  Blockley Hall
423 Guardian Drive
Philadelphia, PA 19104

Phone: 215-898-1560
Fax:   215-573-1203
Email: xwang5 at mail.med.upenn.edu
Website:  http://www.cceb.med.upenn.edu/services/bac/