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Dear list,
I'm having issues in generating an heatmap which occurred only after
the upgrade to ver. 3.1.1
Below you find a very easy example which works in previous R version
3.0.2 but not in ver. 3.1.1 giving the following error.
Error in heatmap.2(t(mtcars), dendrogram = c("col"), Rowv = FALSE,
Colv = as.dendrogram(xClust)) :
Colv dendrogram doesn't match size of x
I've also added sessionInfo() for the NOT WORKING case and WORKING
case.
Can anyone help me to understand why a script that was working 2 weeks
ago isn't working anymore?
Thanks for your help
Remo
data(mtcars)
mtcars
xDist<-dist(mtcars,method="euclidean")
xClust<-hclust(xDist,method="complete")
plot(xClust,labels=FALSE)
heatmap.2(t(mtcars),
dendrogram=c("col"),
Rowv=FALSE,
Colv=as.dendrogram(xClust))
--
__________________________________________________________
Remo Chiozzotto PhD
CNR (National Research Council)
Institute of Agricultural Biology and Biotechnology (IBBA)
Via E. Bassini, 15 - 20133 - Milano (Italy)
Office +39 0223699427
Lab +39 0223699426
Fax +39 0223699411
e-mail: remo.chiozzotto at ibba.cnr.it
skype: remo.chiozzotto
__________________________________________________________
-- output of sessionInfo():
NOT WORKING
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
LC_TIME=it_IT.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=it_IT.UTF-8 LC_MESSAGES=en_US.UTF-8
LC_PAPER=it_IT.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines parallel stats graphics grDevices utils
datasets methods base
other attached packages:
[1] NMF_0.20.5 Biobase_2.24.0 cluster_1.15.2
rngtools_1.2.4 pkgmaker_0.22
[6] registry_0.2 gplots_2.14.0 edgeR_3.6.4
limma_3.20.8 RColorBrewer_1.0-5
[11] ShortRead_1.22.0 GenomicAlignments_1.0.1 BSgenome_1.32.0
Rsamtools_1.16.1 GenomicRanges_1.16.3
[16] GenomeInfoDb_1.0.2 Biostrings_2.32.0 XVector_0.4.0
IRanges_1.22.9 BiocParallel_0.6.1
[21] BiocGenerics_0.10.0
loaded via a namespace (and not attached):
[1] BatchJobs_1.2 BBmisc_1.7 bitops_1.0-6
brew_1.0-6 caTools_1.17 checkmate_1.1
[7] codetools_0.2-8 colorspace_1.2-4 DBI_0.2-7
digest_0.6.4 doParallel_1.0.8 fail_1.2
[13] foreach_1.4.2 gdata_2.13.3 ggplot2_1.0.0
grid_3.1.1 gridBase_0.4-7 gtable_0.1.2
[19] gtools_3.4.1 hwriter_1.3 iterators_1.0.7
KernSmooth_2.23-12 lattice_0.20-29 latticeExtra_0.6-26
[25] MASS_7.3-33 munsell_0.4.2 plyr_1.8.1
proto_0.3-10 Rcpp_0.11.2 reshape2_1.4
[31] RSQLite_0.11.4 scales_0.2.4 sendmailR_1.1-2
stats4_3.1.1 stringr_0.6.2 tools_3.1.1
[37] xtable_1.7-3 zlibbioc_1.10.0
WORKING
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Italian_Italy.1252 LC_CTYPE=Italian_Italy.1252
[3] LC_MONETARY=Italian_Italy.1252 LC_NUMERIC=C
[5] LC_TIME=Italian_Italy.1252
attached base packages:
[1] splines parallel stats graphics grDevices utils
datasets
[8] methods base
other attached packages:
[1] NMF_0.20.5 Biobase_2.22.0 cluster_1.14.4
[4] rngtools_1.2.4 pkgmaker_0.22 registry_0.2
[7] gplots_2.14.1 RColorBrewer_1.0-5 ShortRead_1.20.0
[10] Rsamtools_1.14.3 lattice_0.20-24 Biostrings_2.30.1
[13] GenomicRanges_1.14.4 XVector_0.2.0 IRanges_1.20.6
[16] BiocGenerics_0.8.0 BiocInstaller_1.12.1 edgeR_3.4.2
[19] limma_3.18.13
loaded via a namespace (and not attached):
[1] bitops_1.0-6 caTools_1.17 codetools_0.2-8
[4] colorspace_1.2-4 digest_0.6.4 doParallel_1.0.8
[7] foreach_1.4.2 gdata_2.13.3 ggplot2_1.0.0
[10] grid_3.0.2 gridBase_0.4-7 gtable_0.1.2
[13] gtools_3.4.1 hwriter_1.3 iterators_1.0.7
[16] KernSmooth_2.23-10 latticeExtra_0.6-26 MASS_7.3-29
[19] munsell_0.4.2 plyr_1.8.1 proto_0.3-10
[22] Rcpp_0.11.2 reshape2_1.4 scales_0.2.4
[25] stats4_3.0.2 stringr_0.6.2 tools_3.0.2
[28] xtable_1.7-3 zlibbioc_1.8.0
--
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