Thanks James.

That works perfect for me. And as you rightly said I would need to tinker
things by hand for the QC Report and viewing the intensity of a probe across
arrays.

For QC Report I tried qc.data <- qc(celData) and got the following message:
Error in setQCEnvironment(cdfn) :
  Could not find array definition file ' hugene10stv1.r3cdf.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.

Any pointers on where I could find some information to try things by hand?

Thanks for your time and help.

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


On Tue, Mar 30, 2010 at 10:53 AM, James MacDonald <jmacdon@med.umich.edu>wrote:

> 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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