[BioC] express & summary.stat=li.wong -> error report

cberry@tajo.ucsd.edu cberry@tajo.ucsd.edu
Wed, 13 Nov 2002 09:50:05 -0800 (PST)


I think that error message is what I got in using an Hu6800 chip where
there are (apparently) two probe sets with just one pair. The hack I used
was to insert after this line in fit.li.wong:

  J <- dim(data.matrix)[2]

the following comment and line:

###  The following line is intended to deal with a problem in the
###  treatment of Hu6800 chips. That chip has a couple of probe sets
###  in which there is only one PM-MM pair. Probably, it is just a
###  control region, so I am omitting the fit.li.wong operations for
###  any such probe set

  if (J == 1)  return(list(theta=c(data.matrix),sigma.theta=rep(NA,length(data.matrix))))



On Wed, 13 Nov 2002, Rafael A. Irizarry wrote:

> my guess is that one of those guys was left with just one column (or 
> none) and was turned into a vector. we probably need to add a drop=FALSE 
> somewhere.
> 
> On Wed, 13 Nov 2002, Hinnerk Boriss wrote:
> 
> > Hi there!
> > 
> > I have a statement like this: 
> > 
> > 	data.lwf <- express(data, summary.stat=li.wong)
> > 
> > and I get the following error message:
> > 
> > 	Error in data.matrix[,!phi.outliers] %*% phi[!phi.outliers] :
> > 			non-conformable arguments
> > 
> > What does this error message mean in detail? Does the li.wong routine
> > require to do some outlier checking beforehand? If so, what method is
> > approporiate? Just to mention, I am not a fan of removing outliers.
> > Anyway, How would I find the trouble making values in my data?
> > 
> > Cheers,
> > Hinnerk
> > 
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@stat.math.ethz.ch
> > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> > 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@stat.math.ethz.ch
> http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 

Charles C. Berry                        (858) 534-2098 
                                         Dept of Family/Preventive Medicine
E mailto:cberry@tajo.ucsd.edu	         UC San Diego
http://hacuna.ucsd.edu/members/ccb.html  La Jolla, San Diego 92093-0645