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Question: oposSOM error in UseMethod("layout")
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gravatar for kimagure_
5 months ago by
kimagure_10
kimagure_10 wrote:

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!

 

 

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