[BioC] mas5calls error with YG_S98 CEL files

[Crispin Miller]

Hi,
This bug is, indeed, as you say, due to probes with only one probe/pair.
I'll be uploading a new version of the code next week with this fixed -
I'll post to the list when it's done. I'll also be putting up an updated
version of simpleaffy with rat and yeast chips added to the QC metrics.

Cheers,

Crispin
 

-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Bruz
Marzolf
Sent: 22 September 2004 20:02
To: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] mas5calls error with YG_S98 CEL files

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,
Bruz

> 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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