[BioC] hist and mva.pairs problems

[Laurent Gautier]

On Thu, Dec 05, 2002 at 07:13:50PM -0800, 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:

You are using the Windows version, right ? (Guessing from the fact you mention 'zip' files). I have no easy access to that version now, so I'll try with
Linux.

data(islands)
hist(islands) 

data(affybatch.example)
hist(affybatch.example)

...works here...Could you specify what is the 'basic histogram function' ?



> 
> error in log(x, base) : Non-numeric argument to mathematical function

what does give 'traceback()' just after the error message appears ?




L.



> 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
> 
> 
> Send Bioconductor mailing list submissions to
> 	bioconductor@stat.math.ethz.ch
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> or, via email, send a message with subject or body 'help' to
> 	bioconductor-request@stat.math.ethz.ch
> 
> You can reach the person managing the list at
> 	bioconductor-admin@stat.math.ethz.ch
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bioconductor digest..."
> 
> 
> 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
> 
> 
> 
> --__--__--
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> End of Bioconductor Digest
> 
> 
> This email/fax message, including any attachments, is for the sole use of
> the intended recipient(s) and may contain confidential and privileged
> information.  Any unauthorized review, use, disclosure or distribution is
> prohibited.  If you are not the intended recipient, please contact the
> sender by reply e-mail/fax and destroy all copies of the original message.
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

-- 
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent