[BioC] error while running RMA

[Jeff Lande]

I have been having some problems with the RMA module and I found a
thread in the archives regarding the problem, but I couldn't find any
resolution to it.
 
Does anyone know if this has been resolved?
 
Here is my error message (I am analyzing 9 MOE430 chips using SSH to
connect to a Sun workstation - version 1.8.0 of BioC):
 
> > > > Data <- ReadAffy()
> > > > eset <- rma(Data)
> > > Error in if (a[k] > b[k]) return(1) else if (a[k] < b[k])
return(-1) :
> > >         missing value where TRUE/FALSE needed
> > > In addition: Warning message:
> > > NAs introduced by coercion
 
Below is the thread
 
could you also give us the results of traceback() called right after the
error occurs.
 
btw, it is not generally a good idea to assign the results of a function
to a variable of the same name.
 
 
On Fri, 2003-08-29 at 08:21, Lang Chen wrote:
> Hi, there
> 
> R version 1.71
> BioC version 1.2.
> 
> library(affy)
> data<-ReadAffy()
> rma<-rma(data)
> write.exprs(rma,file="rma.xls")
> 
> Thank you for your help
> 
> Lang Chen
> 
> 
> 
> -----Original Message-----
> From: Ben Bolstad [mailto:bolstad at stat.berkeley.edu
<https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor> ]
> Sent: Friday, August 29, 2003 9:08 AM
> To: Lang Chen
> Subject: Re: [BioC] error while running RMA
> 
> 
> Can you tell me the version of the package that you are using and what
> functions you are calling to compute RMA?
> 
> 
> On Fri, 2003-08-29 at 05:49, Lang Chen wrote:
> > Hi, 
> > 
> > I am running RMA on eight ME 430 chips in the cluster(Linux). I got
the
> > following message.
> > 
> > Error in if (a[k]>b[k] return (1) else if (a[k]<b[k] return (-1) :
> >            missing value where TRUE/FALSE needed
> > In addition: Warning message:
> > NAs introduced by coercion
> > Execution halted
> > 
> > What does it mean? What should I do?
> > 
> > But it works on my PC (Windows 2000 PIII 128M RAM).
> > 
> > Your help is greatly appreciated.
> > 
> > Lang Chen
> > 
> > Research Assistant
> > Department of Biostatistics 
> > Section on Statistical Genetics
> > Ryals Public Health Building, Suite 343A
> > University of Alabama at Birmingham
> > 1530 3rd Ave S
> > Birmingham, Alabama 35294
> > Tel 205-9757772
> > 
> > _______________________________________________
> > Bioconductor mailing list
> >  <https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor>
Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
-- 
Ben Bolstad <
<https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor> bolstad at
stat.berkeley.edu>
 

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