[BioC] Design Matrix Question
Kenny Ye
kye at ams.sunysb.edu
Wed Oct 22 17:55:31 MEST 2003
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
> --------------------------------
>
>
>
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