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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@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 [[alternative HTML version deleted]] _______________________________________________ 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

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@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@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@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 [[alternative HTML version deleted]] _______________________________________________ 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