EGSEA : unable to plot heatmaps.
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Entering edit mode
RV • 0
@rv-10578
Last seen 3.6 years ago

Hi, 

I have been using EGSEA and I very much like it. While everything works just fine, I do have an issue with heat map generation. For both the test data set (built-in) and for my very own data set  I do not get any run time error but do not get any heat maps generated either. Although I do see the legends written out for each of the gene set. When I tried plotting it using the S4 result however, I got an error as follows - 

> plotHeatmap(gsa)
ERROR: plotHeatmap(...) encountered an error:
Error in paste0("Generating heatmap for ", gene.set, " from the collection \n", : argument "gene.set" is missing, with no default

I am not sure where to find the gene.set variable. I would greatly appreciate your help. 

 

Please find attached my Session info. Thanks, RV


> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] Rgraphviz_2.20.0     RColorBrewer_1.1-2   data.table_1.10.4    reshape2_1.4.2       EGSEA_1.4.1          pathview_1.16.5      org.Hs.eg.db_3.4.1  
 [8] topGO_2.28.0         SparseM_1.77         GO.db_3.4.1          graph_1.54.0         AnnotationDbi_1.38.1 IRanges_2.10.2       S4Vectors_0.14.3    
[15] gage_2.26.1          Biobase_2.36.2       BiocGenerics_0.22.0  edgeR_3.18.1         limma_3.32.3        

loaded via a namespace (and not attached):
 [1] nlme_3.1-131             bitops_1.0-6             matrixStats_0.52.2       GSVA_1.24.1              R2HTML_2.3.2             bit64_0.9-7             
 [7] httr_1.2.1               tools_3.4.0              doRNG_1.6.6              R6_2.2.2                 KernSmooth_2.23-15       DBI_0.7                 
[13] lazyeval_0.2.0           colorspace_1.3-2         bit_1.1-12               compiler_3.4.0           pkgmaker_0.22            labeling_0.3            
[19] caTools_1.17.1           KEGGgraph_1.38.1         scales_0.4.1             PADOG_1.18.0             stringr_1.2.0            digest_0.6.12           
[25] XVector_0.16.0           pkgconfig_2.0.1          HTMLUtils_0.1.7          rlang_0.1.2              RSQLite_2.0              hwriter_1.3.2           
[31] gtools_3.5.0             RCurl_1.95-4.8           magrittr_1.5             KEGG.db_3.2.3            Matrix_1.2-10            Rcpp_0.12.12            
[37] munsell_0.4.3            stringi_1.1.5            zlibbioc_1.22.0          gplots_3.0.1             KEGGdzPathwaysGEO_1.14.0 plyr_1.8.4              
[43] globaltest_5.30.0        blob_1.1.0               gdata_2.18.0             lattice_0.20-35          Biostrings_2.44.2        splines_3.4.0           
[49] annotate_1.54.0          KEGGREST_1.16.1          locfit_1.5-9.1           hgu133plus2.db_3.2.3     hgu133a.db_3.2.3         rngtools_1.2.4          
[55] EGSEAdata_1.4.0          codetools_0.2-15         XML_3.98-1.9             GSA_1.03                 metap_0.8                png_0.1-7               
[61] foreach_1.4.3            org.Mm.eg.db_3.4.1       gtable_0.2.0             org.Rn.eg.db_3.4.1       ggplot2_2.2.1            xtable_1.8-2            
[67] survival_2.41-3          tibble_1.3.3             iterators_1.0.8          registry_0.3             memoise_1.1.0            safe_3.16.0             
[73] GSEABase_1.38.0   

EGSEA R bioconductor • 512 views
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1
Entering edit mode
RV • 0
@rv-10578
Last seen 3.6 years ago

This was a problem in my graphics viewer. 

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