bug in Glimma - anno can't have T/F
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Jenny Drnevich ★ 2.0k
@jenny-drnevich-2812
Last seen 6 months ago
United States

Hi Matt,

Great to see you again at BioC2016! And thanks so much for telling me about Glimma - the interactive visualizations are amazing and my clients will love them. I got the devel version to work yesterday but I was playing around with it this morning and found a problem - if you pass the anno argument a data.frame that has a column containing TRUE/FALSE values, nothing appears when you open the HTML. Sorry I can't send a working example but you should be able to verify on your own. I switched the T/F to character "yes"/"no" and then the html showed the interactive plot.

Thanks again for a great addition to the limma/edgeR/DESeq2 analysis pipelines!

Jenny

sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

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

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

other attached packages:
 [1] Glimma_1.1.3          org.Hs.eg.db_3.3.0    AnnotationDbi_1.35.3  rgl_0.95.1441         rtracklayer_1.33.8   
 [6] GenomicRanges_1.25.8  GenomeInfoDb_1.9.2    IRanges_2.7.11        S4Vectors_0.11.7      gplots_3.0.1         
[11] magrittr_1.5          WGCNA_1.51            fastcluster_1.1.20    dynamicTreeCut_1.63-1 Biobase_2.33.0       
[16] BiocGenerics_0.19.1   edgeR_3.15.0          limma_3.29.12        

loaded via a namespace (and not attached):
 [1] Category_2.39.0               bitops_1.0-6                  matrixStats_0.50.2            doParallel_1.0.10            
 [5] RColorBrewer_1.1-2            httr_1.2.0                    tools_3.3.1                   R6_2.1.2                     
 [9] KernSmooth_2.23-15            rpart_4.1-10                  Hmisc_3.17-4                  DBI_0.4-1                    
[13] colorspace_1.2-6              nnet_7.3-12                   gridExtra_2.2.1               GGally_1.1.0                 
[17] DESeq2_1.13.6                 preprocessCore_1.35.0         chron_2.3-47                  graph_1.51.0                 
[21] ggbio_1.21.2                  caTools_1.17.1                scales_0.4.0                  genefilter_1.55.2            
[25] RBGL_1.49.1                   stringr_1.0.0                 digest_0.6.9                  Rsamtools_1.25.0             
[29] foreign_0.8-66                R.utils_2.3.0                 AnnotationForge_1.15.4        XVector_0.13.2               
[33] dichromat_2.0-0               htmltools_0.3.5               ensembldb_1.5.8               BSgenome_1.41.2              
[37] impute_1.47.0                 PFAM.db_3.3.0                 RSQLite_1.0.0                 BiocInstaller_1.23.4         
[41] shiny_0.13.2                  GOstats_2.39.1                gtools_3.5.0                  BiocParallel_1.7.4           
[45] acepack_1.3-3.3               R.oo_1.20.0                   VariantAnnotation_1.19.4      RCurl_1.95-4.8               
[49] GO.db_3.3.0                   Formula_1.2-1                 Matrix_1.2-6                  Rcpp_0.12.5                  
[53] munsell_0.4.3                 R.methodsS3_1.7.1             stringi_1.1.1                 SummarizedExperiment_1.3.6   
[57] zlibbioc_1.19.0               plyr_1.8.4                    AnnotationHub_2.5.4           grid_3.3.1                   
[61] gdata_2.17.0                  lattice_0.20-33               Biostrings_2.41.4             splines_3.3.1                
[65] GenomicFeatures_1.25.14       annotate_1.51.0               locfit_1.5-9.1                knitr_1.13                   
[69] geneplotter_1.51.0            reshape2_1.4.1                codetools_0.2-14              biomaRt_2.29.2               
[73] XML_3.98-1.4                  biovizBase_1.21.0             latticeExtra_0.6-28           data.table_1.9.6             
[77] httpuv_1.3.3                  foreach_1.4.3                 gtable_0.2.0                  reshape_0.8.5                
[81] ggplot2_2.1.0                 mime_0.4                      xtable_1.8-2                  survival_2.39-5              
[85] OrganismDbi_1.15.1            iterators_1.0.8               GenomicAlignments_1.9.4       cluster_2.0.4                
[89] interactiveDisplayBase_1.11.3 GSEABase_1.35.0 

Glimma • 1.2k views
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Shian Su ▴ 40
@shian-su-9869
Last seen 1 day ago
Walter and Eliza Hall Institute of Medi…

Thanks for bringing this to my attention, it's definitely an unintended bug, it will be fixed in the next patch which I hope to push out by the end of the week.

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Great! Looking forward to continued improvements – everyone here thought the interactive graphs were amazing! Thanks again, Jenny From: shians [bioc] [mailto:noreply@bioconductor.org] Sent: Monday, June 27, 2016 9:14 PM To: Zadeh, Jenny Drnevich <drnevich@illinois.edu> Subject: [bioc] C: bug in Glimma - anno can't have T/F Activity on a post you are following on support.bioconductor.org<https: urldefense.proofpoint.com="" v2="" url?u="&lt;a href=" http:="" <a="" href="http://https-3A__support.bioconductor.org" rel="nofollow">https-3A__support.bioconductor.org"="" rel="nofollow">https-3A__support.bioconductor.org&d=CwMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=6-Bh1FprrmfLCzuKMeeZ1IaQQqjRPj_xNcuCh6hXgSU&m=F_GMGANvfWCWKgQvNWwKbpHKPfHbzHH9zhcZBZMHUTU&s=Ga55jI3ux800ncg3qva-oBX4ahIAHpQkWyO2kxTYX58&e="> User shians<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_u_9869_&amp;d=CwMCaQ&amp;c=8hUWFZcy2Z-Za5rBPlktOQ&amp;r=6-Bh1FprrmfLCzuKMeeZ1IaQQqjRPj_xNcuCh6hXgSU&amp;m=F_GMGANvfWCWKgQvNWwKbpHKPfHbzHH9zhcZBZMHUTU&amp;s=zy6valo6UWYHijIDMayI-cc8Uu1ljUQcwdOGCCix-x8&amp;e="> wrote Comment: bug in Glimma - anno can't have T/F<https: urldefense.proofpoint.com="" v2="" url?u="https-3A__support.bioconductor.org_p_84318_-2384347&amp;d=CwMCaQ&amp;c=8hUWFZcy2Z-Za5rBPlktOQ&amp;r=6-Bh1FprrmfLCzuKMeeZ1IaQQqjRPj_xNcuCh6hXgSU&amp;m=F_GMGANvfWCWKgQvNWwKbpHKPfHbzHH9zhcZBZMHUTU&amp;s=HwC96HVP22vd7ZYC51nByndYSEgr0eCXrF5yBSNxJUE&amp;e=">: Thanks for bringing this to my attention, it's definitely an unintended bug, it will be fixed in the next patch which I hope to push out by the end of the week. ________________________________ Post tags: Glimma You may reply via email or visit C: bug in Glimma - anno can't have T/F
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