[BioC] Problem with Hopach: "Error in dmat[ord, ]"

[Paolo Innocenti]

Hi all,

I'm experiencing this problem with hopach package. The following code 
runs just fine in a fresh session, but gives an error (see below) in my 
working directory:

 > require(hopach)
 > data(golub)
 > vars <- apply(golub, 1, var)
 > subset <- vars > quantile(vars, (nrow(golub) - 200)/nrow(golub))
 > golub.subset <- golub[subset, ]
 > gnames.subset <- golub.gnames[subset, ]
 > gene.dist <- distancematrix(golub.subset, "cosangle")
 > gene.hobj <- hopach(golub.subset, dmat = gene.dist)
Error in dmat[ord, ] :
   element 1 is empty;
    the part of the args list of 'is.logical' being evaluated was:
    (j)
 > traceback()
4: dmat[ord, ]
3: dmat[ord, ]
2: orderelements(cuttree, data, rel = ord, d, dmat)
1: hopach(golub.subset, dmat = gene.dist)
 > sessionInfo()
R version 2.9.0 (2009-04-17)
x86_64-unknown-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base

other attached packages:
[1] hopach_2.4.0    Biobase_2.4.1   cluster_1.11.13 RSQLite_0.7-1
[5] DBI_0.2-4

loaded via a namespace (and not attached):
  [1] affy_1.22.0           affyio_1.12.0         AnnotationDbi_1.6.0
  [4] drosophila2.db_2.2.11 grid_2.9.0            lattice_0.17-22
  [7] lme4_0.999375-28      Matrix_0.999375-26    MCMCglmm_1.09
[10] preprocessCore_1.6.0  tools_2.9.0


The "real" code I am running, that gives the same error message, is the 
following:

 > hopach.eset.antag <- eset[which(featureNames(eset) %in% rtop.int$ID),]
 > antag.dist.matrix <- distancematrix(exprs(hopach.eset.antag), "cosangle")
 > hopach.clusters.antag <- hopach(hopach.eset.antag, 
dmat=antag.dist.matrix)
Error in dmat[ord, ] :
   element 1 is empty;
    the part of the args list of 'is.logical' being evaluated was:
    (j)

I haven't found the same error reported in the ML.
Cheers,
paolo



-- 
Paolo Innocenti
Department of Animal Ecology, EBC
Uppsala University
Norbyvägen 18D
75236 Uppsala, Sweden