[BioC] affy, se.exprs slot.

[Laurent Gautier]

On Tue, Nov 19, 2002 at 11:57:07AM +0100, Laurent Buffat wrote:
> 
> Hi,
> 
> The standart error returned by the se.exprs slot are for a given gene, the
> same on the different arrays.
> Is it  correct ? or there is a bug in the se.exprs slot ?
> 
> Example :
> 
>  data(Dilution)
>  e <- express(Dilution)
>  se.exprs(e)[1,]
> 
>  se.exprs(e)[1,] return 0.04187569 for all the arrays ...
> 
> Thanks
> 
> L.  Buffat
> 

Dear Laurent,

The se.exprs returned by 'express' depends on the method used
to summarize the probe intensities by one expression value.
The default 'summary' function for 'express' is 'medianpolish'
(unlike what is stated in the man pages. This will be fixed
shortly), which gives one rough estimate of se for each gene.

Apparently this is not a bug (but I might be corrected on this
very same list when the West starts the day).

Hopin' it helps,


Laurent

 

--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent