[BioC] Very odd error while using globaltest()

[J.Oosting at lumc.nl]

Could you please state the sessionInfo() output. I could not reproduce this problem in either R2.4 or R2.5 with their respective bioconductor and globaltest versions. In older versions of the globaltest there has been a problem with using numeric vectors as class variable. You could try it with a chararcter vector.

The source code for globaltest is available from the bioconductor website, or when the package is loaded you can type 'globaltest' without any braces and see the sourcecode.

Jan

> Tae-Hoon Chung
> Sent: vrijdag 30 maart 2007 2:12
> I¹ve been trying to use globaltest() function whole day but 
> one problem kept coming up. I had a gene expression matrix 
> made using RMA and concatenated the whole matrix into a 54675 
> x 23 dimensional matrix. And I prepared another sample class 
> vector with the size of 23. When I ran the globaltest() 
> function as follows, I¹ve got a very odd error:
> 
> ...
> > sample.ok <- ... (a sample name vector with 23 elements) 
> n.norm <- 4 
> > n.acc <- length(sample.ok) - n.norm cls <- c(rep(1, n.norm), rep(2, 
> > n.acc)) gt.grp <- globaltest(rma.mat[,sample.ok], cls)
> Error in app[1, ] <- c(rep(TRUE, top), rep(FALSE, bottom)) :
>     number of items to replace is not a multiple of replacement length
> >
> 
> The R system keeps complaining with the same message but I 
> can¹t figure out why. There was no way I could access the 
> source code of the globaltest so I don¹t have any clue where 
> this error could have happened yet. Any ideas?
> 
> Thank you very much
> 
> Tae-Hoon Chung
> 
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