[BioC] Siggenes/SAM Error

[Holger Schwender]

Pretty strange bug. I will fix it in the next few days. Should then be available in the devel section of Bioconductor. Should be available in siggenes version 1.15.1 and later.

Best,
Holger



-------- Original-Nachricht --------
> Datum: Wed, 2 Jul 2008 15:55:29 -0700
> Von: "D F" <dflab1 at gmail.com>
> An: bioconductor at stat.math.ethz.ch
> Betreff: [BioC] Siggenes/SAM Error

> Hi,
> 
> I'm new to Bioconductor and R and I apologize if this is absolutely
> obvious
> (as it must be), however, the issue escapes me. I wish to run SAM on a set
> of 5 replicates over two classes. I've loaded normalized and logged
> expression data into a matrix (called data) and ran the commands below,
> which results in an error. Could you please advise on what the problem
> might
> be?
> 
> Thanks.
> De
> 
> > dim(data)
> [1] 22690     5
> > dim(gene_names)
> [1] 22690     1
> > rownames(data) <- as.matrix(gene_names)
> > sam.out <- sam(data, c(0,0,1,1,1))
> 
> We're doing 10 complete permutations
> 
> Error in d.perm[, i] <- sort(tmp$t.num/(tmp$t.denum + s0)) :
>   number of items to replace is not a multiple of replacement length
> 
> In addition: Warning message:
> There are 127 variables with zero variance. These variables are removed,
> and their d-values are set to NA.
> 
> 	[[alternative HTML version deleted]]
> 
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