 
Hello All
 
I  am helping someone analyse their two-colour microarrays and would
appreciate some advice.
 
Looking at the limma Users guide I need an approach that is a
cross/mixture of  "7.3 Common Reference Designs" and "8.8 Time Course
Experiments", or something similar.
 
Question1 : Is the "8.8 Time Course Experiments" section aimed at
Affymetrix type arrays? i.e. Not two colour arrays.
 
Question 2: If the answer to question 1 is "No" how do you adapt for two
colourarrays? i.e. to include the Reference data? I notice that the end
of section "8.6 Several Groups" implies you can easily adapt by using
modelMatrix. Is that all that is required?
 
My Targets file looks something like below.
 
Is it valid to do something like the following to get a comparison
between the two time intervals and the ctrl and test treatments?  Or is
it more complex:
 
#############################################################
 
# 7.3 Common Reference Designs
design <- modelMatrix(targets, ref="Reference")
 
# linear model fit 
fit<-lmFit(MA.nba,design)
 
# contrast matrix
contrast.matrix<-makeContrasts(ctrlt1, ctrlt24, testt1, testt24, ctrlt24
+ testt24 - ctrlt1 - testt1, testt1 + testt24 - ctrlt24 - ctrlt1,
levels=design)
fit2<- contrasts.fit(fit, contrast.matrix)
 
etc
 
################################################################

Thanks for any help.
 
Regards
 
 
John Seers
 
 
P.S. If this question looks familiar I have asked a similar question
before but this is a different set of slides. 
 
 
 
 
 
SlideNumber FileName Cy5 Cy3
51 T24CTRL3.gpr ctrlt24 Reference
52 T24CTRL2.gpr ctrlt24 Reference
53 T24CTRL1.gpr ctrlt24 Reference
54 T24TEST4.gpr testt24 Reference
55 T24TEST3.gpr testt24 Reference
56 T24TEST2.gpr testt24 Reference
57 T24TEST1.gpr testt24 Reference
105 T24CTRL4.gpr ctrlt24 Reference
545 T1CTRL1.gpr ctrlt1 Reference
546 T1TEST3.gpr testt1 Reference
547 T1TEST2.gpr testt1 Reference
558 T1CTRL3.gpr ctrlt1 Reference
559 T1CTRL2.gpr ctrlt1 Reference
592 T1TEST4.gpr testt1 Reference
593 T1TEST1.gpr testt1 Reference    
 
 
 
 
 
---

John Seers
Institute of Food Research
Norwich Research Park
Colney
Norwich
NR4 7UA
 

tel +44 (0)1603 251497
fax +44 (0)1603 507723
e-mail john.seers@bbsrc.ac.uk                         
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<http://www.ifr.ac.uk/edisclaimer/>  
 
Web sites:

www.ifr.ac.uk <http://www.ifr.ac.uk/>    
www.foodandhealthnetwork.com <http://www.foodandhealthnetwork.com/> 
 

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