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

[Paolo Innocenti]

Hi Vincent,

thanks for the help,
I emptied the R workspace and tried again. Both the example and my own 
code work now. Something in the workspace was probably conflicting with 
it. No idea what.

I am happy with that at the moment...

Thanks,
paolo

 > require(hopach)
Loading required package: hopach
Loading required package: cluster
 > 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)
 > 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)
 > traceback()
No traceback available
 > 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 utils     datasets  methods   base

other attached packages:
[1] hopach_2.4.0         cluster_1.11.13      limma_2.18.0
[4] drosophila2cdf_2.4.0 vsn_3.12.0           affy_1.22.0
[7] Biobase_2.4.1

loaded via a namespace (and not attached):
[1] affyio_1.12.0        grid_2.9.0           lattice_0.17-22
[4] preprocessCore_1.6.0 tools_2.9.0
 >



Vincent Carey wrote:
> alas, i cannot replicate this with the devel version
> 
>  > sessionInfo()
> R version 2.10.0 Under development (unstable) (2009-04-06 r48294)
> i386-apple-darwin9.6.0
> 
> locale:
> C
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base    
> 
> other attached packages:
> [1] hopach_2.5.0    Biobase_2.3.10  cluster_1.11.12
> 
> loaded via a namespace (and not attached):
> [1] tools_2.10.0
> 
> in which your example runs to completion. 
> 
> On Wed, May 20, 2009 at 6:30 AM, Paolo Innocenti 
> <paolo.innocenti at ebc.uu.se <mailto:paolo.innocenti at ebc.uu.se>> wrote:
> 
>     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
>     <http://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
> 
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> 
> 
> 
> 
> -- 
> Vincent Carey, PhD
> Biostatistics, Channing Lab
> 617 525 2265

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