[BioC] Modelmatrix

[Jason Skelton]

You're not using the 'parameters' argument to modelMatrix() correctly.  The main point though is
that there is no need to take special action to allow for different numbers of replicates.  This
is accommodated automatically in the course of an ordinary analysis.

Gordon


Dear Gordon,

Sorry for being slow about this....  
If in an extreme example you had three biological replicates A,B and C
and for biological replicate A you had 12 replicates
but for biological replicates B & C you only had 1 replicate
Surely the model that is fitting the data for biological 
replicate A would be over emphasized relative to the others?


The Experiment we are actually concerned with is descibed in the following targets list:
(sorry its a bit complicated)

Cy3	Cy5
pig1aA	wtA
pig2A	pig1aA
mybA	pig2A
tulipA	mybA
kal1A	tulipA
wtA	kal1A
pig1aA	kal1A
pig2A	wtA
mybA	pig1aA
tulipA	pig2A
kal1A	mybA
wtA	tulipA
tulipC	pig1aC
arpA	wtC
arpB	mybB
arpC	tulipC
wtB	pig1aB
wtC	pig2C
mybC	wtC
mybB	tulipB
pig1aC	arpC
pig1aB	pig2B
pig2B	arpB
pig2C	mybC
tulipB	wtB 
 
Where A, B, and C designate the different biological replicates. So 
replicate A is covered by twice the number of slides as B or C.
We are use to experiments with similar numbers of replicates within a loop design.
However with this slightly scewed experiment we are worried that the data isn't accurately modelled.

many thanks

Jason 


-- 
--------------------------------
Jason Skelton
Pathogen Microarrays
Wellcome Trust Sanger Institute
Hinxton
Cambridge
CB10 1SA

Tel +44(0)1223 834244 Ext 7123
Fax +44(0)1223 494919