[BioC] hist and mva.pairs problems

[Vawter, Marquis]

I have d/l the latest R1.6.1 and Affy 1.1  Attached is a histogram from
newly U95A chips. It seems that the basic histogram function is gone, and
the mva.pairs function keeps giving the error:

Error in log(x, base) : Non-numeric argument to mathematical function
There seems to be major problems with the Affy1.1 basic functions although
the zip file indicates that these are 12/5/02 implementations.  I will await
to see if others are experiencing similar things. Thanks, Mark Vawter

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Today's Topics:

   1. Does computeExprSet bug affect rma function? (Rohan Williams)
   2. Re: Does computeExprSet bug affect rma function? (Ben Bolstad)

--__--__--

Message: 1
Date: Thu, 5 Dec 2002 10:56:56 +1100
To: bioconductor@stat.math.ethz.ch
From: Rohan Williams <r.williams@centenary.usyd.edu.au>
Subject: [BioC] Does computeExprSet bug affect rma function?

Dear All,

I was wondering whether the recently identified problem with 
'computeExprSet' is known to affect the rma function? (from reading 
the documentation I gather it doesn't)

Apologies for the hassle, but I have an abstract due in the next 
couple of days and would prefer not to recalculate everything unless 
absolutely necessary.

Best,

Rohan Williams


--__--__--

Message: 2
Subject: Re: [BioC] Does computeExprSet bug affect rma function?
From: Ben Bolstad <bolstad@stat.berkeley.edu>
To: Rohan Williams <r.williams@centenary.usyd.edu.au>
Cc: bioconductor@stat.math.ethz.ch
Date: 04 Dec 2002 17:45:43 -0800

On Wed, 2002-12-04 at 15:56, Rohan Williams wrote:
> Dear All,
> 
> I was wondering whether the recently identified problem with 
> 'computeExprSet' is known to affect the rma function? (from reading 
> the documentation I gather it doesn't)
> 
> Apologies for the hassle, but I have an abstract due in the next 
> couple of days and would prefer not to recalculate everything unless 
> absolutely necessary.
> 
> Best,
> 
> Rohan Williams
> 

The rma() function from 1.1 has never has this problem and was not
affected by this bug. However, if you calculated RMA using expresso you
might have problems.

Ben



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