[BioC] limma, is there a limited number of levels for a factor?

[James W. MacDonald]

Hi Steve,

On 8/7/2010 2:32 PM, steve shen wrote:
> Hello,
>
> Does anyone know if there is a limited number of levels for a factor or
> how to reset the defaults? I have a two factor experiment which one
> factor has 2 levels while another has 7 levels. I got errors while I run
> following analysis. Please help. Thanks,

The limit to the number of factors is dependent on the number of samples 
you have. In your case, you are fooling R into creating a design matrix 
that is not of full rank.

Anyway, I am not sure you want to use the 'phe' factor. I am guessing 
that you have some sort of control sample that is not treated, and then 
six other sample types that are treated with the same thing, but in a 
different vehicle. In which case I think you just want

design <- model.matrix(~tr)

which is full rank. The baseline in this case would be the untreated 
sample, and the coefficients for everything else would be the comparison 
of the treatment/vehicle combination to the untreated sample.

Best,

Jim


>
> Steve
>
>  > design <- model.matrix(~phe+tr)
>  > design
> (Intercept) pheVehicle tr1-Ant tr2-TCDD tr3-DIM tr4-Ago tr5-CH tr6-DMSO
> 1 1 0 0 0 0 0 0 0
> 2 1 0 0 0 0 0 0 0
> 3 1 0 0 0 0 0 0 0
> 4 1 1 0 0 0 0 0 1
> 5 1 1 0 0 0 0 0 1
> 6 1 1 0 0 0 0 0 1
> 7 1 1 0 1 0 0 0 0
> 8 1 1 0 1 0 0 0 0
> 9 1 1 0 1 0 0 0 0
> 10 1 1 0 0 1 0 0 0
> 11 1 1 0 0 1 0 0 0
> 12 1 1 0 0 1 0 0 0
> 13 1 1 0 0 0 1 0 0
> 14 1 1 0 0 0 1 0 0
> 15 1 1 0 0 0 1 0 0
> 16 1 1 0 0 0 0 1 0
> 17 1 1 0 0 0 0 1 0
> 18 1 1 0 0 0 0 1 0
> 19 1 1 1 0 0 0 0 0
> 20 1 1 1 0 0 0 0 0
> 21 1 1 1 0 0 0 0 0
> attr(,"assign")
> [1] 0 1 2 2 2 2 2 2
> attr(,"contrasts")
> attr(,"contrasts")$phe
> [1] "contr.treatment"
>
> attr(,"contrasts")$tr
> [1] "contr.treatment"
>
>  > fit <- lmFit(x.data, design)
> Coefficients not estimable: tr6-DMSO
> Warning message:
> Partial NA coefficients for 29198 probe(s)
>  > fit2 <- eBayes(fit)
> Warning message:
> In ebayes(fit = fit, proportion = proportion, stdev.coef.lim =
> stdev.coef.lim) :
> Estimation of var.prior failed - set to default value
>  > sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-apple-darwin9.8.0
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] limma_3.2.2
>
> loaded via a namespace (and not attached):
> [1] tools_2.10.1
>
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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