[BioC] cl Vector

[Kasper Daniel Hansen]

On Nov 2, 2005, at 7:51 AM, Assa Yeroslaviz wrote:

> Hi,
>
> is it possible to read a file for the sam calculation with the gene  
> names in the
> same table.
> The first column was with gene names, the next four were with  
> experiments and
> the next 14 were the controls.
> I've tried this way:
>
>> last.data <- read.delim2("AE0625419_genenames.txt")
>> last.out <- sam(last.data, AE0627999.cl, B=20,  
>> gene.names=matrix_all_names[,2])
>
> But i get this message:
> Fehler in adjust.for.mt(data, cl, var.equal = var.equal) :
>         The length of cl must be equal to the number of columns of  
> data.
> Zusätzlich: Warning messages:
> 1: NAs durch Umwandlung erzeugt
> 2: There are 22811 genes with at least one missing expression value.
> The NAs are replaced by the gene-wise mean.
> 3: 22791 of the 22811 genes with at least one NA have no and 20  
> have one
> non-missing expression value.
> All these 22811 genes are removed, and their d-values are set to NA.
>
> Is there a way of telling sam to ignore the first columns for the  
> cl-vector?

If I understand you correctly, cl is a matrix (or a data.frame). if  
that is true, just selct the appropriate column by
   AE0627999$columnName
or
   AE0627999[,1] (for the first column)

Kasper



> THX,
>
> Assa
>
> --
> Assa Yeroslaviz
> Lötzenerstr. 15
> 51373 Leverkusen
>
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