[BioC] Very odd error while using globaltest()

J.Oosting at lumc.nl J.Oosting at lumc.nl
Fri Mar 30 09:40:09 CEST 2007

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.


> 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
> 	[[alternative HTML version deleted]]

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