[BioC] Design Matrix Question

[Jason Skelton]

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