[BioC] factorial experiment matrix design

[Gordon K Smyth]

> Date: Wed, 04 May 2005 17:37:35 +0300
> From: Mikko Arvas <Mikko.Arvas at vtt.fi>
> Subject: [BioC] factorial experiment matrix design
> To: bioconductor at stat.math.ethz.ch
>
> Hi,
>
> reading the BioC list I see that things like this are asked often, but I am
> sorry I just can't get this. Could somebody show me how to do it:
>
> I have a microarray experiment with 2 strains and 3 time points from each,
> so I would like to do 2x3 factorial experiment
> to get all the genes that change in strain A (or B) during time series (10,
> 30, 60 min) and between strains in all the time points.
>
> So trying to follow limma guide, the design matrix object would be
> something like this (with 2 repeats for each):
>
>  > dQex
>     (Intercept) Qexa10 Qexa30 Qexa60 Qexb10 Qexb30
> 1            1      1      0      0      0      0
> 2            1      1      0      0      0      0
> 3            1      0      1      0      0      0
> 4            1      0      1      0      0      0
> 5            1      0      0      1      0      0
> 6            1      0      0      1      0      0
> 7            1      0      0      0      1      0
> 8            1      0      0      0      1      0
> 9            1      0      0      0      0      1
> 10           1      0      0      0      0      1
> 11           1      0      0      0      0      0
> 12           1      0      0      0      0      0
> attr(,"assign")
> [1] 0 1 1 1 1 1
> attr(,"contrasts")
> attr(,"contrasts")$Qex
>      a10 a30 a60 b10 b30
> a10   1   0   0   0   0
> a30   0   1   0   0   0
> a60   0   0   1   0   0
> b10   0   0   0   1   0
> b30   0   0   0   0   1
> b60   0   0   0   0   0
>
> What kind of contrast (or as well design) matrix do I need to get all the
> changing genes out?

YOu need to pick out the 5 non-intercept coefficients:

cont.matrix <- rbind(0,diag(5))

Gordon

> Cheers,
> Mikko
>
>
>
> Mikko Arvas
> VTT Biotechnology
>
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> from start of year 2005.
>
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