[BioC] report a possible buy in edgeR

[Mark Robinson]

Hi Shan,

I don't see the problem here.  Can you elaborate?

Why should it be the sum of a matrix?  Keep in mind also that this function is run using apply() to each column of the count matrix.

Best,
Mark

On 08.07.2012, at 23:44, wang peter wrote:

> dear all:
>      i read the source coding of edgeR_2.4.6
> the function of .calcFactorWeighted has some problem
> 
> .calcFactorWeighted <- function(obs, ref, logratioTrim=.3,
> sumTrim=0.05, doWeighting=TRUE, Acutoff=-1e10) {
> 
>  if( all(obs==ref) )
>    return(1)
> 
>  obs <- as.numeric(obs)
>  ref <- as.numeric(ref)
> 
>  nO <- sum(obs)  # this is should be the sum of matrix
>  nR <- sum(ref)
> 
> 
> from the formula in the cited paper, it seems it should be column sum
> -- 
> shan gao
> Room 231(Dr.Fei lab)
> Boyce Thompson Institute
> Cornell University
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