[BioC] cdfName/annotation variants for hgu133a?

[James W. MacDonald]

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
> 
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-- 
James W. MacDonald
University of Michigan
Affymetrix and cDNA Microarray Core
1500 E Medical Center Drive
Ann Arbor MI 48109
734-647-5623



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