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

[Rafael A. Irizarry]

i think the hg6800 chip has a one probe probe set which makes li.wong
break down.

On Thu, 14 Nov 2002, Hinnerk Boriss wrote:

> Yes, I do work with Hu6800 chips and thanks, I get past that error
> message, however, I run into a new one: 
> 	Error in apply(resid[, !phi.outliers]^2, 1, sum) :
> 		dim(x) must have a positive length
> 
> > traceback()
> 8: stop("dim(X) must have a positive length")
> 7: apply(resid[, !phi.outliers]^2, 1, sum)
> 6: fit.li.wong(t(data.matrix), remove.outliers, normal.array.quantile, 
>        normal.resid.quantile, large.threshold, large.variation, 
>        outlier.fraction, delta, maxit, outer.maxit, verbose)
> 5: FUN(X[[4318]], ...)
> 4: lapply(as.list(X), FUN, ...)
> 3: sapply(data.lst, summary.stat, ...)
> 2: t(sapply(data.lst, summary.stat, ...))
> 1: express(NormLemonData, summary.stat = li.wong)
> 
> 
> Any suggestions on that one?
> 
> Cheers,
> Hinnerk
> 
> 
> > 
> > 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(dat
> a.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
> > > > 
> > > > 
> > > > _______________________________________________
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> > 
> > 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
> > 
> >  
> > 
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>