[BioC] HT_HG-U133A_EA

[Hassane, Duane]

Shiju,

Putting this back on list, it appears that you are missing the required cdf environment.  Try ...

source("http://www.bioconductor.org/biocLite.R")
biocLite("u133aaofav2cdf")

Best,

Duane





_________________________________________________
Duane Hassane, Ph.D.
Center for Pediatric Biomedical Research
University of Rochester Medical Center
Rochester, New York 14642

-----Original Message-----
From: Shiju Zhang [mailto:SZHANG at ms.soph.uab.edu]
Sent: Monday, March 05, 2007 6:23 PM
To: Hassane, Duane
Subject: RE: [BioC] HT_HG-U133A_EA


Hi Duane,

Thank you for your discussion. The cel data is available in NCBI
database "GEO DataSets" (search for GSM119084.CEL) Here is the message I
got when using ReadAffy and justRMA.

> estrogen <- ReadAffy(filenames="GSM119084.CEL")
> estrogen

Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered:
Specified environment does not contain U133AAofAv2
Library - package u133aaofav2cdf not installed
Data for package affy did not contain u133aaofav2cdf
Bioconductor - u133aaofav2cdf not available
AffyBatch object
size of arrays=744x744 features (4329 kb)
cdf=U133AAofAv2 (??? affyids)
number of samples=1
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered:
Specified environment does not contain U133AAofAv2
Library - package u133aaofav2cdf not installed
Data for package affy did not contain u133aaofav2cdf
Bioconductor - u133aaofav2cdf not available
In addition: Warning message:
missing cdf environment ! in: show(list())


> estrogen <- justRMA(filenames="GSM119084.CEL")
Error in getCdfInfo(object) : Could not obtain CDF environment, problems
encountered:
Specified environment does not contain U133AAofAv2
Library - package u133aaofav2cdf not installed
Data for package affy did not contain u133aaofav2cdf
Bioconductor - u133aaofav2cdf not available


Thanks again!

Shiju Zhang

-----Original Message-----
From: Hassane, Duane [mailto:Duane_Hassane at URMC.Rochester.edu] 
Sent: Monday, March 05, 2007 2:38 PM
To: Shiju Zhang; bioconductor at stat.math.ethz.ch
Subject: RE: [BioC] HT_HG-U133A_EA

Shiju,

More info would help.  I've not encountered a problem with CELs of that
type using justRMA().  

Thanks,

Duane Hassane





-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch]On Behalf Of Shiju Zhang
Sent: Monday, March 05, 2007 11:53 AM
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] HT_HG-U133A_EA


Hi,

 

It seems to me that affy can't read gene chip .cel data with chip type
Affymetrix GeneChip HT-HG_U133A Early Access Array. Anybody has any
idea?

 

Thanks.

 

Shiju Zhang


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