Question: cdfName/annotation variants for hgu133a?
0
gravatar for peter.warren@verizon.net
14.3 years ago by
Hello, I am trying to write an R function that detects the chip type of an exprset passed in, then executes different code depending on chip type. In particular, I want to detect the HGU133A, HGU133 Plus 2.0, and HGU133B. Does anyone know if there is a limited set of allowable strings for the cdfName/annotation name of these three chips? I would need to check for, and accept, all of them, I believe. A little detail... The input exprset has been generated by running functions like rma(), expresso(), mas5(), etc., on an AffyBatch created from CEL files from many possible sources (not under my control). In my code, I'm using "annotation(myExprset)" to get the chip type string. In the case of the HGU133A, I have now seen two strings in the annotation slot: "hgu133atag" and "hgu133a". If my code doesn't detect the right string, it exits with error message. Thanks! - Peter Warren Wyeth Research Cambridge, MA, USA
annotation hgu133a hgu133b • 461 views
ADD COMMENTlink modified 14.3 years ago by James W. MacDonald51k • written 14.3 years ago by peter.warren@verizon.net40
Answer: cdfName/annotation variants for hgu133a?
0
gravatar for James W. MacDonald
14.3 years ago by
United States
James W. MacDonald51k wrote:
peter.warren at verizon.net wrote: > Hello, > > I am trying to write an R function that detects the chip type of an > exprset passed in, then executes different code depending on chip > type. In particular, I want to detect the HGU133A, HGU133 Plus 2.0, > and HGU133B. Does anyone know if there is a limited set of allowable > strings for the cdfName/annotation name of these three chips? I would > need to check for, and accept, all of them, I believe. The results of annotation(myExprset) will be unique for each chip type. The reason you have seen two different strings is because the underlying chips were also different. hgu133a is the name given for the HG-U133A chip, and hgu133atag is the name for the HG-U133A_TAG chip, which AFAIK was only used for internal testing by Affy (the U133 latin square study). So your choices will be hgu133a, hgu133b, hgu133plus2, and hgu133atag (if you are doing work with the latin square data set). Best, Jim > > A little detail... The input exprset has been generated by running > functions like rma(), expresso(), mas5(), etc., on an AffyBatch > created from CEL files from many possible sources (not under my > control). In my code, I'm using "annotation(myExprset)" to get the > chip type string. In the case of the HGU133A, I have now seen two > strings in the annotation slot: "hgu133atag" and "hgu133a". If my > code doesn't detect the right string, it exits with error message. > > Thanks! - Peter Warren Wyeth Research Cambridge, MA, USA > > _______________________________________________ Bioconductor mailing > list Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald University of Michigan Affymetrix and cDNA Microarray Core 1500 E Medical Center Drive Ann Arbor MI 48109 734-647-5623 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
ADD COMMENTlink written 14.3 years ago by James W. MacDonald51k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 199 users visited in the last hour