Hi all,

We are trying to use justPlier() and have some difficulties finding the 
options described in the Affy's technical note 
(<http://www.affymetrix.com/support/technical/technotes/plier_technote.pdf>http://www.affymetrix.com/support/technical/technotes/plier_technote.pdf) 
in the plier implementation you've done. In particular, we don’t see how 
are the background options implemented. How exactly do the 'usemm' and 
'usemodel' arguments in justPlier() treat the background, compared the 
PM-MM, PM-B, PM only, and MM treated as PM options described in the 
technical note ? For instance, what argument should be chosen to treat MM 
as PM ? Also, there's no information given about the parameters presumed to 
optimize the plier model. Are the default parameters suitable, and in which 
circumstances are we supposed to modify them ? For instance, a member of 
this list mentioned last October that setting concpenalty=0.1 removed a lot 
of the artefacts of different fold change between plier and RMA. Is this 
really necessary ?
Thanks,
Marie-Paule


Marie-Paule ROTH
Directrice de Recherche
INSERM U 563
CPTP - Bātiment B
CHU Purpan
BP 3028
F - 31024 Toulouse Cedex 3

Tel. (33) 5 62 74 45 08
Fax: (33) 5 62 74 45 58
E-mail: roth@cict.fr


	[[alternative HTML version deleted]]

