[BioC] vsn in BioConductor 1.2

[w.huber at dkfz-heidelberg.de]

Hi Isaac,

does your data matrix contain Inf (infinity) or an excessive number of 0s
(e.g.  through "flooring" the negative values?). If there are infinities
in the data, this will probably also lead to an infinite likelihood, which
could explain your error message.

If there are other singularities (e.g.  if a whole column of the data
matrix has the same value), this may also lead to infinite values in the
likelihood calculations.

If these suggestions do not lead to the solution of your problem, you
could send me your data matrix (anonymized) and I could try to figure out
where things go wrong.  The calculations in vsn are not that complicated.
This may be useful in making it more robust or at least in making it
produce more intelligible error messagess.

Note that I'll be away from my email from now till Thursday.

Best regards
  Wolfgang

-------------------------------------
Wolfgang Huber
Division of Molecular Genome Analysis
German Cancer Research Center
Heidelberg, Germany
Phone: +49 6221 424709
Fax:   +49 6221 42524709
Http:  www.dkfz.de/mga/whuber
-------------------------------------


On Mon, 21 Jul 2003, Isaac Neuhaus wrote:

> Wolfgang:
>
> I chopped some of the ouptup here is everything.
>
> Isaac
>
>  > data <- read.table("file.msk", header=T, sep = "\t", row.names=1)
>  > data <- as.matrix(data)
>  > vsn.data <- vsn(data)
> vsn is working on a 4992 x 376 matrix, with lts.quantile=0.5; please
> wait for 11 dots:
> .Error in optim(par = p0, fn = ll, gr = grll, method = "L-BFGS-B",
> control = control,  :
>         non-finite value supplied by optim
>