[BioC] vsn in BioConductor 1.2

[Isaac Neuhaus]

w.huber at dkfz-heidelberg.de wrote:

>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.
>
Yes, In some cases it contains up to 75% of 0s. I will exclude these 
samples and try to run the vsn again.
Thanks for your help.

Isaac

>
>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
>>
>>    
>>