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kimagure_
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@kimagure_-12870
Last seen 7.6 years ago
I'm trying to run oposSOM on a matrix of expression data and ran into an error:
[INFO] Processing Geneset Profiles and Maps [INFO] Writing: Unnamed - Results/Geneset Analysis/*.{csv,pdf} Error in UseMethod("layout") : no applicable method for 'layout' applied to an object of class "c('double', 'numeric')"
Commands I used:
preferences <- list(indata = exprs(eset), group.labels = rep(c("label1", "label2"), 5), group.colors = rep(c("red2", "blue2"), 5)) opnew <- opossom.new(preferences) opossom.run(opnew)
Session info is as follows:
sessionInfo() R version 3.3.2 (2016-10-31) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS release 6.8 (Final) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C [10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] grid stats4 parallel stats graphics grDevices utils datasets [9] methods base other attached packages: [1] biomaRt_2.30.0 oposSOM_1.12.0 [3] igraph_1.0.1 pheatmap_1.0.8 [5] annotate_1.52.1 XML_3.98-1.5 [7] mogene20sttranscriptcluster.db_8.5.0 org.Mm.eg.db_3.4.0 [9] AnnotationDbi_1.36.2 ComplexHeatmap_1.12.0 [11] reshape_0.8.6 reshape2_1.4.2 [13] BiocInstaller_1.24.0 pd.mogene.2.0.st_3.14.1 [15] oligo_1.38.0 RSQLite_1.0.0 [17] DBI_0.5-1 Biostrings_2.42.1 [19] XVector_0.14.0 IRanges_2.8.1 [21] S4Vectors_0.12.0 genefilter_1.56.0 [23] plotly_4.5.2 scatterplot3d_0.3-39 [25] ggplot2_2.2.1 oligoClasses_1.36.0 [27] limma_3.30.11 Biobase_2.34.0 [29] BiocGenerics_0.20.0 loaded via a namespace (and not attached): [1] nlme_3.1-131 pixmap_0.4-11 bitops_1.0-6 [4] RColorBrewer_1.1-2 httr_1.2.1 prabclus_2.2-6 [7] GenomeInfoDb_1.10.3 tools_3.3.2 R6_2.2.0 [10] affyio_1.44.0 KernSmooth_2.23-15 lazyeval_0.2.0 [13] colorspace_1.3-2 trimcluster_0.1-2 nnet_7.3-12 [16] GetoptLong_0.1.5 gridExtra_2.2.1 bit_1.1-12 [19] preprocessCore_1.36.0 fdrtool_1.2.15 diptest_0.75-7 [22] scales_0.4.1 DEoptimR_1.0-8 robustbase_0.92-7 [25] mvtnorm_1.0-5 stringr_1.1.0 digest_0.6.12 [28] base64enc_0.1-3 htmltools_0.3.5 htmlwidgets_0.8 [31] GlobalOptions_0.0.10 shape_1.4.2 jsonlite_1.2 [34] mclust_5.2.2 dendextend_1.4.0 dplyr_0.5.0 [37] RCurl_1.95-4.8 magrittr_1.5 modeltools_0.2-21 [40] Matrix_1.2-8 Rcpp_0.12.7 munsell_0.4.3 [43] viridis_0.3.4 ape_4.1 stringi_1.1.2 [46] whisker_0.3-2 MASS_7.3-45 SummarizedExperiment_1.4.0 [49] zlibbioc_1.20.0 flexmix_2.3-13 plyr_1.8.4 [52] affxparser_1.46.0 lattice_0.20-34 splines_3.3.2 [55] circlize_0.3.9 GenomicRanges_1.26.2 rjson_0.2.15 [58] fpc_2.1-10 codetools_0.2-15 foreach_1.4.3 [61] gtable_0.2.0 purrr_0.2.2 tidyr_0.6.0 [64] kernlab_0.9-25 assertthat_0.1 xtable_1.8-2 [67] ff_2.2-13 class_7.3-14 survival_2.40-1 [70] viridisLite_0.1.3 SparkR_2.0.2 tibble_1.2 [73] iterators_1.0.8 som_0.3-5.1 cluster_2.0.5 [76] fastICA_1.2-0
Any ideas on how to solve this error? Thank you in advance!