error on heatmap
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Guest User ★ 12k
@guest-user-4897
Last seen 7.1 years ago
Dear Biocondutor users, I would like to plot the heatmap using metagenomeSeq package, I used the same example dataset and same R scripts from package tutorial, but it has the error message when I do the heatmap. Please see R scripts and error message below: > data(mouseData) > trials = pData(mouseData)$diet > heatmapColColors = brewer.pal(12, "Set3")[as.integer(factor(trials))] > heatmapCols = colorRampPalette(brewer.pal(9, "RdBu"))(50) > plotMRheatmap(obj = mouseData, n = 200, cexRow = 0.4, cexCol = 0.4,trace = "none", col = heatmapCols, ColSideColors = heatmapColColors) Error in heatmap.2(mat2, ...) : lazy-load database 'P' is corrupt In addition: Warning messages: 1: In heatmap.2(mat2, ...) : restarting interrupted promise evaluation 2: In heatmap.2(mat2, ...) : internal error -3 in R_decompress1 Thanks for the help, I really appreciate it. -- output of sessionInfo(): > sessionInfo() R version 3.0.2 (2013-09-25) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] metagenomeSeq_1.4.0 matrixStats_0.8.14 limma_3.18.13 Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 [7] RColorBrewer_1.0-5 vegan_2.0-10 lattice_0.20-27 permute_0.8-3 Heatplus_2.8.0 gplots_2.12.1 loaded via a namespace (and not attached): [1] bitops_1.0-6 caTools_1.16 gdata_2.13.2 grid_3.0.2 gtools_3.3.1 KernSmooth_2.23-10 R.methodsS3_1.6.1 [8] tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.
PROMISE metagenomeSeq PROMISE metagenomeSeq • 844 views
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@joseph-nathaniel-paulson-6442
Last seen 4.6 years ago
United States
Hi there, Some others have had similar error issues with lazy-load database. Have you tried restarting R? That's what the users recommend in this thread: http://r.789695.n4.nabble.com/weird-error-with-a-lazyload-RData-file- in-a-package-td4662836.html . I don't have the same issue with the release, nor, developer versions. Best, - Joseph Paulson On Sun, Mar 9, 2014 at 8:02 PM, guest [guest] <guest@bioconductor.org>wrote: > > Dear Biocondutor users, > > I would like to plot the heatmap using metagenomeSeq package, I used the > same example dataset and same R scripts from package tutorial, but it has > the error message when I do the heatmap. Please see R scripts and error > message below: > > > data(mouseData) > > trials = pData(mouseData)$diet > > heatmapColColors = brewer.pal(12, "Set3")[as.integer(factor(trials))] > > heatmapCols = colorRampPalette(brewer.pal(9, "RdBu"))(50) > > plotMRheatmap(obj = mouseData, n = 200, cexRow = 0.4, cexCol = 0.4,trace > = "none", col = heatmapCols, ColSideColors = heatmapColColors) > > Error in heatmap.2(mat2, ...) : lazy-load database 'P' is corrupt > In addition: Warning messages: > 1: In heatmap.2(mat2, ...) : restarting interrupted promise evaluation > 2: In heatmap.2(mat2, ...) : internal error -3 in R_decompress1 > > Thanks for the help, I really appreciate it. > > > > -- output of sessionInfo(): > > > sessionInfo() > R version 3.0.2 (2013-09-25) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > base > > other attached packages: > [1] metagenomeSeq_1.4.0 matrixStats_0.8.14 limma_3.18.13 > Biobase_2.22.0 BiocGenerics_0.8.0 BiocInstaller_1.12.0 > [7] RColorBrewer_1.0-5 vegan_2.0-10 lattice_0.20-27 > permute_0.8-3 Heatplus_2.8.0 gplots_2.12.1 > > loaded via a namespace (and not attached): > [1] bitops_1.0-6 caTools_1.16 gdata_2.13.2 grid_3.0.2 > gtools_3.3.1 KernSmooth_2.23-10 R.methodsS3_1.6.1 > [8] tools_3.0.2 > > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
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