[BioC] error in estimateVarianceFunctions

[Steve Lianoglou]

Hi,

On Wed, Sep 28, 2011 at 1:12 PM, Dawei Li <dawei_lili at yahoo.com> wrote:
>
> Dear Simon:
>
>
>  The following is my code:
>
> library("DESeq")
> countsTable<-read.table("mycount.dat", sep = "\t",header=TRUE, stringsAsFactors=TRUE, row.names="gene")
> conds <- factor(c("T","C"))
> cds   <- newCountDataSet( countsTable, conds )
> cds   <- estimateSizeFactors( cds)
> cds   <- estimateVarianceFunctions(cds,method=TRUE)
>
> I got the following error message:
>
> Error in match.arg(method) : 'arg' must be NULL or a character vector

I suspect this is because of the value you are giving for the `method`
argument to `estimateVarianceFunctions`.

Take a closer look at the help from ?estimateVarianceFunctions ... it
doesn't seem like "TRUE" is a valid value for that argument.

This is true for my version of DESeq, though (1.4.1) -- you still
haven't given us the output of sessionInfo() so it's making it
difficult to diagnose your problems ...

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact