[BioC] limma, is there a limited number of levels for a factor?
steve shen
ssshen at mit.edu
Sat Aug 7 20:32:01 CEST 2010
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,
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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