[BioC] Design Matrix Question

[Kenny Ye]

this is what I would put your experiment in a design matrix

Slide Treatment Dye
1	DIF1	-1
2       DIF1     1
.
.
6	DIF1	-1
7	DIF2	-1
.
.
12	DIF2	-1
13	DIF3	-1
14	DIF3	 1
.
.
18	DIF3	-1

Then you can use ANOVA to compare the different drugs.

Kenny


Kenny Ye
Assistant Professor
Department of Applied Math and Statistics
SUNY at  Stony Brook
Stony Brook, New York 11794-3600
Phone (631)632-9344
Fax   (631)632-8490

On Wed, 22 Oct 2003, Jason Skelton wrote:

> Kenny Ye wrote:
> 
> >what is your treatments?  and what is the level 0? would you please give
> >more details on your experiment?
> >
> >Kenny
> >
> Hi kenny
> 
> Apologies my understanding of how a matrix works isn't necessarily correct
> The 0 indicates that they are NOT present in a particular treatment
> 
> 
> I'm currently using R: Version 1.7.1
> 
> DIF1,2 and 3 are different but similar drugs...............
> 
> Slides 1-6 are treatment 1 (DIF1) Vs No treatment
> Slide1 Cy5/Cy3 (DIF1/no treatment)
> Slide2 Cy3/Cy5 (DIF1/no treatment)
> Slide3 Cy5/Cy3 (DIF1/no treatment)
> Slide4 Cy3/Cy5 (DIF1/no treatment)
> Slide5 Cy3/Cy5 (DIF1/no treatment)
> Slide6 Cy5/Cy3 (DIF1/no treatment)
> 
> Slides 7-12 are treatment 2 (DIF2) Vs No treatment
> Slide7 Cy5/Cy3 (DIF2/no treatment)
> Slide8 Cy3/Cy5 (DIF2/no treatment)
> Slide9 Cy5/Cy3 (DIF2/no treatment)
> Slide10 Cy3/Cy5 (DIF2/no treatment)
> Slide11 Cy3/Cy5 (DIF2/no treatment)
> Slide12 Cy5/Cy3 (DIF2/no treatment)
> 
> Slides 13-18 are treatment 3(DIF3) Vs No treatment
> Slide13 Cy5/Cy3 (DIF3/no treatment)
> Slide14 Cy3/Cy5 (DIF3/no treatment)
> Slide15 Cy5/Cy3 (DIF3/no treatment)
> Slide16 Cy3/Cy5 (DIF3/no treatment)
> Slide17 Cy3/Cy5 (DIF3/no treatment)
> Slide18 Cy5/Cy3 (DIF3/no treatment)
> 
> I'd obviously like to compare across the different treatments DIF1,2 and 3
> 
> 
> 
> Thanks
> 
> Jason
> 
> 
> >>Hi
> >>
> >>I'd like to construct a design matrix similar to the following but have 
> >>no idea how to do it
> >>
> >>I'm trying the model.matrix function
> >>
> >>Slide	Treatment1	Treatment2	Treatment3
> >>1	-1		0		0
> >>2	1		0		0
> >>3	-1		0		0
> >>4	1		0		0	
> >>5	1		0		0
> >>6	-1		0		0
> >>7	0		-1		0
> >>8	0		1		0
> >>9	0		-1		0
> >>10	0		1		0
> >>11	0		1		0
> >>12	0		-1		0
> >>13	0		0		-1
> >>14	0		0		1
> >>15	0		0		-1
> >>16	0		0		1
> >>17	0		0		1
> >>18	0		0		-1
> >>
> >>-1 represents Cy5/cy3
> >>1 represents Cy3/Cy5
> >>
> >>    
> >>
> 
> 
> -- 
> --------------------------------
> Jason Skelton
> Pathogen Microarrays
> Wellcome Trust Sanger Institute
> Hinxton
> Cambridge
> CB10 1SA
> 
> Tel +44(0)1223 834244 Ext 7123
> Fax +44(0)1223 494919
> --------------------------------
> 
> 
>