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

[Laurent Gautier]

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
 >