[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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