bug in Glimma - anno can't have T/F
Entering edit mode
Jenny Drnevich ★ 2.0k
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!


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

[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 • 656 views
Entering edit mode
Shian Su ▴ 40
Last seen 14 months 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.

Entering edit mode
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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