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

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Paolo Innocenti ▴ 320

@paolo-innocenti-2191

Last seen 9.6 years ago

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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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 Norbyv?gen 18D 75236 Uppsala, Sweden

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ADD COMMENT • link updated 14.9 years ago by Vincent J. Carey, Jr. 6.7k • written 14.9 years ago by Paolo Innocenti ▴ 320

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Vincent J. Carey, Jr. 6.7k

@vincent-j-carey-jr-4

Last seen 6 weeks ago

United States

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@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_IDEN TIFICATION=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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265 [[alternative HTML version deleted]]

ADD COMMENT • link 14.9 years ago Vincent J. Carey, Jr. 6.7k

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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_N AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI FICATION=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 > Norbyv?gen 18D > 75236 Uppsala, Sweden > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > -- > Vincent Carey, PhD > Biostatistics, Channing Lab > 617 525 2265 -- Paolo Innocenti Department of Animal Ecology, EBC Uppsala University Norbyv?gen 18D 75236 Uppsala, Sweden

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