[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
> >
> >
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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