[BioC] Design Matrix Question

[Gordon K Smyth]

This isn't a design matrix, it's a data matrix (from which a design matrix
might be computed).

Assuming the intention is to set up an design matrix for use in limma, the
recommended command is

   designMatrix(targets, ref)

where 'targets' has a columns 'cy3' giving the channel1 treatment and
'cy5' giving the channel2 treatment and 'ref' is just the name of the
common reference.

In limma 1.3.0 (available next week) there is a function 'readTargets' for
reading in the target info.  In the meantime, just set up the info in
Excel, write to disk as a tab-delimited file, read into R using
'read.table' with 'as.is=TRUE'.

Gordon

> 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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