[BioC] Affy : checkSlotAssignment() Error

[Sundaram, Shyam (NIH/CIT)]

Just as I gave this msg I find a simliar issue in May 2002 archive 
About a similar problem and the solution ...



[BioC] Question about affy 
Rafael A. Irizarry rafa@jhu.edu 
Wed, 15 May 2002 11:00:33 -0400 (EDT) 

this is a bug. we assume that you will provide phenoData (look at the help 
file or the Biobase description).
if you have phenotypic data and it has more than 2 covariantes add it. 
that will solve your problem.
otherwise, while we fix it, here is a work around




So I will give it a shot and see if it works ...

Thanks
Shyam

-----Original Message-----
From: Sundaram, Shyam (NIH/CIT) 
Sent: Wednesday, November 06, 2002 1:26 PM
To: Bioconductor (E-mail)
Subject: [BioC] Affy : checkSlotAssignment() Error


Hi:
Thanks in advance for helping.
I was able to load successfully the "HG-U133A" CEL and CDF file through the
ReadAffy() method into a "plob" object. When I tried to convert it to the
exprSet using the express() function I was faced with the following error
message.
Normalizing Data
Error in checkSlotAssignment(object, name, value) : 
        Value supplied is not valid for slot "pm", is(value, "matrix") is
not TRUE
To make sure the cel,cdf files are loaded properly I tried to load them
through the read.celfile, read.cdffile methods and they seem to do so with
out errors.
Any suggestions on what might be the cause of the problem?


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