[BioC] hist and mva.pairs problems

[Rafael A. Irizarry]

the package changed quite a bit. the new vignette explains some of the 
changes and also gives examples. we believe its an improvement... but it 
is different. sorry about that. 

mva.pairs is no longer a method (we tried to reduce the number of methods 
for technical reasons). mva.pairs now takes matrices so you need to 
extract them yourself using intensity(), pm() and/or mm(). 

as for the histogram, we believe the new 
method is an improvement of the previous one. you can easily get 
the old  histograms using

pms <- pm(Data)
for(i in 1:ncol(pms))
	hist(pms[,i]))

and the mvas using

o <- sample(1:nrow(pms),1000) ##otherwise loess takes for ever.
mva.pairs(pms[o,])


here, Data is an AffyBatch instance.

hope this helps,
rafael



On Thu, 5 Dec 2002, Vawter, Marquis wrote:

> 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
> 
> -----Original Message-----
> From: bioconductor-request@stat.math.ethz.ch
> [mailto:bioconductor-request@stat.math.ethz.ch]
> Sent: Thursday, December 05, 2002 3:00 AM
> To: bioconductor@stat.math.ethz.ch
> Subject: Bioconductor digest, Vol 1 #180 - 2 msgs
> 
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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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