[BioC] vsn in BioConductor 1.2

[Isaac Neuhaus]

Hi Wolfgang:

I am also getting the same error with a matrix that is 4992 x 376. Here 
are the R commands:

 > 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:
.

and then dies. Any suggestions?

after I do a traceback I get the following:

 > traceback()
2: optim(par = p0, fn = ll, gr = grll, method = "L-BFGS-B", control = 
control,
       lower = plower)
1: vsn(data)

Any help is greatly appreciated.

Isaac


w.huber at dkfz-heidelberg.de wrote:

>Hi Charles,
>
>vsn is a normalization method that brings the different columns (colors,
>arrays) of an expression matrix on the same scale. As input, it takes an
>n*d matrix, with d>=2. You passed it a matrix with d=1. Apparently this
>results in some of the likelihood calculations becoming singular, hence
>the error message you received.
>
>Action plan:
>1. For you: read the paper on vsn, then call it with expression matrices
>of size d>=2.
>
>2. For me: fix vsn so that it throws an intelligible error message if
>called with d<=1.
>
>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 Thu, 17 Jul 2003, White, Charles E WRAIR-Wash DC wrote:
>
>  
>
>>Could someone help me interpret (develop an action plan to correct ...) the
>>error message that follows?
>>
>>
>>
>>Thanks.
>>
>>
>>
>>    
>>
>>>Monkey.sub<-Monkey.expr[!is.na(Monkey.matrix[,1]),1]
>>>      
>>>
>>>Monkey.sub
>>>      
>>>
>>Expression Set (exprSet) with
>>
>>      13838 genes
>>
>>      1 samples
>>
>>             phenoData object with 6 variables and 1 cases
>>
>>       varLabels
>>
>>            : Slide
>>
>>            : FileName
>>
>>            : Cy3
>>
>>            : Cy5
>>
>>            : date
>>
>>            : Comments
>>
>>    
>>
>>>Monkey.sub<-exprs(Monkey.expr[!is.na(Monkey.matrix[,1]),1])
>>>      
>>>
>>>Monkey.vsn<-vsn(Monkey.sub)
>>>      
>>>
>>vsn is working on a 13838 x 1 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,  :
>>
>>      L-BFGS-B needs finite values of fn
>>
>>
>>	[[alternative HTML version deleted]]
>>
>>    
>>
>
>_______________________________________________
>Bioconductor mailing list
>Bioconductor at stat.math.ethz.ch
>https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>  
>