[BioC] mas5calls error with YG_S98 CEL files

Bruz Marzolf bmarzolf at systemsbiology.org
Wed Sep 22 21:02:24 CEST 2004

Upon further investigation, it appears that failure of mas5calls to work with YG_S98 chips is due to these yeast chips containing probe sets which only have 1 probe pair each. Curious about how GCOS handles these probe sets, I checked and it appears that probe sets with 1 probe pair always receive a p-value of either 0.25 or 0.75.

Could a solution/work-around for this problem be implemented? I'm guessing that the person who originally wrote the code will have the best idea of how this 1 probe pair scenario ought to be dealt with.

Best wishes,

> Date: Mon, 20 Sep 2004 14:34:38 -0700
> From: "Bruz Marzolf" <bmarzolf at systemsbiology.org>
> Subject: [BioC] mas5calls error with YG_S98 CEL files
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <BFBA7186C5B3CB4C8EA0B509FA9090B304EB01 at exchange.systemsbiology.net>
> Content-Type: text/plain;	charset="iso-8859-1"
> Hi all,
> I've encountered trouble when using mas5calls on CEL files 
> from YG_S98 chips:
> 	data <- ReadAffy(filenames =  cel.file.name)
> 	PACalls <- mas5calls(data)
> 	Getting probe level data...
> 	Computing p-values
> 	Making P/M/A Calls
> 	Error in if (y < alpha1) { : missing value where 
> TRUE/FALSE needed
> Both the release and developmental version of the 'affy' 
> package produce this same error, but only with YG_S98 chips 
> (same code works fine on HG-U133_Plus_2 or Mouse430_2 chips). 
>  Has anyone encountered this before?
> Thanks!
> Bruz

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