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

[Paolo Innocenti]

Dear Vincent and list,

hopefully I managed to provide a non-working example. It looks like the 
lme4 (the lme4-required package Matrix in particular) causes some 
incompatibilities:

library(lme4)
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)


produces this on my computer:

 > library(Matrix)
Loading required package: lattice

Attaching package: 'Matrix'


	The following object(s) are masked from package:stats :

	 xtabs


	The following object(s) are masked from package:base :

	 rcond

 > require(hopach)
Loading required package: hopach
Loading required package: cluster
Loading required package: Biobase

Welcome to Bioconductor

   Vignettes contain introductory material. To view, type
   'openVignette()'. To cite Bioconductor, see
   'citation("Biobase")' and for packages 'citation(pkgname)'.

 > 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)
 > 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       Biobase_2.4.1      cluster_1.11.13 
Matrix_0.999375-24
[5] lattice_0.17-22

loaded via a namespace (and not attached):
[1] grid_2.9.0  tools_2.9.0



While the same code - without calling lme4 - works smoothly.
Can anyone suggest a workaround?

Best,
paolo


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