[BioC] negative values in from pmonly in dChip

[Laurent Gautier]

On Tue, Jun 24, 2003 at 12:01:22PM -0700, Wenqiong Chen wrote:
> Hi, everybody:
> Can someone point to me that if it is possible to get negative values from
> the following command?
> expresso(data, normalize.method="invariantset", bg.correct=F,
> pmcorrect.method="pmonly", summary.method="liwong")
> 
> I thought that if I used "pmonly" there should be no negative values,
> especially when no background correction was applied. Did I miss anything? I
> am sure I did.
> Thanks a lot for your help!
> wenqiong
> 

The steps 'normalize.method="invariantset"' and 'summary.method="liwong"'
are the two places were negative values *could* "appear" (depending on
your particular dataset, but I did not check how likely this could happen)...
and there is also the possibility to have negative values in the CEL files
(who knows).

You can run the diffrent steps constituting expresso individually and 
find out...



Hopin' it helps,



L.