[BioC] Limma, lmFit "subscript out of bounds" error
Emmanuel Levy
emmanuel.levy at gmail.com
Tue May 10 19:57:51 CEST 2005
Hello,
I am working with 5 affymetrix arrays: 1 wild type and 4 mutants, all
differents (no replicates).
I think that is the reason why when I run lmFit I get a "subscript out
of bound" error.
I guess one can't fit a linear model with 1 point only.
If it is the case, is there any way around? What would you recommend
to analyse these arrays?
Thank you very much in advance for your help,
Emmanuel
---------- more details -------------------------------------------------------
R: 2.0.1
Package: limma
Version: 1.8.16
Date: 2005/01/09
Package: affy
Version: 1.5.8-1
Date: 2004-10-20
My phenoData is as follow:
> pData(eset2)
pheno
C1 WT
C2 MU1
C3 MU2
C4 MU3
C5 MU5
The design matrix as follow:
> design
WT MU1 MU2 MU3 MU4
1 1 0 0 0 0
2 0 1 0 0 0
3 0 0 1 0 0
4 0 0 0 1 0
5 0 0 0 0 1
attr(,"assign")
[1] 1 1 1 1 1
attr(,"contrasts")
attr(,"contrasts")$f
[1] "contr.treatment"
When I run lmFit, I get an error:
> fit = lmFit(eset2, design)
Error in inherits(x, "data.frame") : subscript out of bounds
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