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

[Gordon K Smyth]

Dear Laurent,

Thanks for bringing this to my attention.  It's an embarassing bug.

You are using treat() as intended.  Here's a (not very elegant) workaround 
while I fix it properly:

   fit <- lmFit(y,design)
   trfit <- treat(fit)
   eb <- eBayes(fit)
   trfit$t <- eb$t
   trfit$lods <- eb$lods
   topTable(trfit,coef=2)

As you probably already realize, there is no point in using treat() unless 
you set a fold-change cutoff.  Otherwise the results are the same as using 
eBayes().

Best wishes
Gordon

> Date: Sat, 13 Jun 2009 13:05:22 +0200
> From: Laurent Gautier <laurent at cbs.dtu.dk>
> Subject: [BioC] Error when calling LIMMA's topTable() with an object
> 	returned by treat()
> To: "bioconductor mail list bioconductor at stat.math.ethz.ch"
> 	<bioconductor at stat.math.ethz.ch>
>
> 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