[BioC] Error when calling LIMMA's topTable() with an object returned by treat()

[Saroj K Mohapatra]

Hi Laurent:

How about using decideTests on trfit?

 > decideTests(trfit[,2])
TestResults matrix
Gene 1 Gene 2 Gene 3 Gene 4 Gene 5
     1      1      0      0      0
95 more rows ...

Best,

Saroj

Laurent Gautier wrote:
> Dear list,
>
>
> Calling LIMMA's topTable() function with an object returned by
> treat() generates an error:
>
> Error in dim(data) <- dim : attempt to set an attribute on NULL
>
>
> # example
>
> sd <- 0.3*sqrt(4/rchisq(100,df=4))
> y <- matrix(rnorm(100*6,sd=sd),100,6)
> rownames(y) <- paste("Gene",1:100)
> y[1:2,4:6] <- y[1:2,4:6] + 2
> design <- cbind(Grp1=1,Grp2vs1=c(0,0,0,1,1,1))
> options(digit=3)
>
> fit <- lmFit(y,design)
> trfit <- treat(fit)
> topTable(trfit,coef=2)
>
>
> Does anyone have a workaround ?
>
>
>
> Laurent
>
>
> > sessionInfo()
> R version 2.9.0 (2009-04-17)
> i386-apple-darwin8.11.1
>
> locale:
> C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] Biostrings_2.12.1    IRanges_1.2.1        lattice_0.17-22 
> preprocessCore_1.6.0 limma_2.18.0         Biobase_2.4.1
>
> loaded via a namespace (and not attached):
> [1] grid_2.9.0
> >
>
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