[BioC] express & summary.stat=li.wong -> error report
Hinnerk Boriss
boriss@izbi.uni-leipzig.de
Thu, 14 Nov 2002 14:17:21 +0100
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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> >
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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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