[BioC] Error in getCdfInfo(object)

[James MacDonald]

Hi Arun,

Try

celData <- ReadAffy(cdfname = "hugene10stv1.r3cdf")

Also note that much of the functionality of simpleaffy (and possibly affyQCReport) are predicated on the chip having MM probes, which the HuGene chip does not, so you will be better off doing things by hand.

Best,

Jim

James W. MacDonald, M.S.
Biostatistician
Douglas Lab
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
>>> Arun A K  03/29/10 11:01 AM >>>
Hi

I tried the following steps:

biocLite("hgu133plus2cdf")

library(affy)
library(simpleaffy)
library(affyQCReport)
setwd("/temp/Cel-Data")
celData <- ReadAffy()
sampleNames(celData)
hist(celData)

I get the following error when I try hist(celData):

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

I looked up for the missing package i.e. hugene10stv1cdf at
http://www.bioconductor.org/packages/release/data/annotation/ and the
closest I could find was
http://www.bioconductor.org/packages/release/data/annotation/html/hugene10stv1.r3cdf.html,
which I installed. But I still get the error.

I am new to R so I might have done some thing naive. Please let me know
where I have gone wrong.

Thanks for your time.

Arun A K
Graduate Student
Department of Computer Science
Indiana University, Bloomington

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