The window opens and it can't load the data - dds and vst provided

[devang-mehta]

I'm running the program using: pcaExplorer(dds=dds, dst=vst) where dds and vst were generated using DEseq. But when the pcaExplorer window opens it can't load the data. It used to work a few months ago so I'm not sure what changed.

[federicomarini]

Hi, can it be related to this?

https://github.com/federicomarini/pcaExplorer/issues/6

[devang-mehta]

thanks. I tried re-installing the package from bio conductor but I still get the same issue

Best, Devang

---

Dr. Devang Mehta Postdoctoral Fellow

CCIS 5-051 Department of Biological Sciences University of Alberta www.uhriglab.com http://www.uhriglab.com/ www.devang.bio http://www.devang.bio/

On Sep 24, 2019, at 4:22 PM, Federico Marini notifications@github.com wrote:

Hi, can it be related to this?

6 https://github.com/federicomarini/pcaExplorer/issues/6

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/federicomarini/pcaExplorer/issues/10?email_source=notifications&email_token=AHBVATAAANLXM7XXLO5M3JDQLKHK5A5CNFSM4I2FN3B2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7P7RUY#issuecomment-534771923, or mute the thread https://github.com/notifications/unsubscribe-auth/AHBVATCAVEKWCF5UTKDEXWLQLKHK5ANCNFSM4I2FN3BQ.

[federicomarini]

Can you provide me at least a screenshot and the full sessionInfo?

[federicomarini]

In the meanwhile: I edited the title of the issue to make it more informative

[devang-mehta]

thanks. here's the screenshot:

> dds <- DESeqDataSetFromTximport(txi.sum, sampleTable, ~condition)
using counts and average transcript lengths from tximport
> dds<-DESeq(dds, fitType = "local" )
estimating size factors
using 'avgTxLength' from assays(dds), correcting for library size
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
> resultsNames(dds)
[1] "Intercept"                            "condition_rve_ED_30_vs_rve_ED_0"      "condition_rve_EN_0_vs_rve_ED_0"       "condition_rve_EN_30_vs_rve_ED_0"     
[5] "condition_wildtype_ED_0_vs_rve_ED_0"  "condition_wildtype_ED_30_vs_rve_ED_0" "condition_wildtype_EN_0_vs_rve_ED_0"  "condition_wildtype_EN_30_vs_rve_ED_0"
> vst <- vst(dds, blind=FALSE)
-- note: fitType='parametric', but the dispersion trend was not well captured by the
   function: y = a/x + b, and a local regression fit was automatically substituted.
   specify fitType='local' or 'mean' to avoid this message next time.
> #plotPCA(rld, intgroup="condition", ntop=Inf)
> pcaExplorer(dds = dds, dst=vst)

Listening on http://127.0.0.1:7861

[federicomarini]

Hmm, weird.

Two things:

• does the console tell you anything relevant while the app is running?
• does the same happen if you load the demo data? (ok, three: what's the sessionInfo()?)

[devang-mehta]

1. Nothing else on the console apart from the listening message.
2. The demo data doesn't load. Nothing happens when I click the button to load the demo data.
3. Session info:

   
   `> sessionInfo()
   R version 3.5.2 (2018-12-20)
   Platform: x86_64-apple-darwin15.6.0 (64-bit)
   Running under: macOS High Sierra 10.13.6

Matrix products: default BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages: [1] BiocInstaller_1.32.1 shiny_1.3.2 biomaRt_2.38.0 topGO_2.34.0 SparseM_1.77
[6] GO.db_3.7.0 graph_1.60.0 PCAtools_0.99.13 cowplot_1.0.0 lattice_0.20-38
[11] reshape2_1.4.3 ggrepel_0.8.1 ggplot2_3.2.1 pcaExplorer_2.8.1 DEVis_1.0.1
[16] ensembldb_2.6.8 AnnotationFilter_1.6.0 GenomicFeatures_1.34.8 DESeq2_1.22.2 SummarizedExperiment_1.12.0 [21] DelayedArray_0.8.0 BiocParallel_1.16.6 matrixStats_0.55.0 GenomicRanges_1.34.0 GenomeInfoDb_1.18.2
[26] readr_1.3.1 AnnotationDbi_1.44.0 IRanges_2.16.0 S4Vectors_0.20.1 Biobase_2.42.0
[31] BiocGenerics_0.28.0 tximport_1.10.1

loaded via a namespace (and not attached): [1] GOstats_2.48.0 backports_1.1.4 Hmisc_4.2-0 NMF_0.21.0 plyr_1.8.4 igraph_1.2.4.1
[7] lazyeval_0.2.2 GSEABase_1.44.0 shinydashboard_0.7.1 splines_3.5.2 crosstalk_1.0.0 gridBase_0.4-7
[13] digest_0.6.21 foreach_1.4.7 htmltools_0.3.6 magrittr_1.5 checkmate_1.9.4 memoise_1.1.0
[19] cluster_2.1.0 doParallel_1.0.15 limma_3.38.3 Biostrings_2.50.2 annotate_1.60.1 prettyunits_1.0.2
[25] colorspace_1.4-1 blob_1.2.0 xfun_0.9 dplyr_0.8.3 jsonlite_1.6 crayon_1.3.4
[31] RCurl_1.95-4.12 genefilter_1.64.0 zeallot_0.1.0 survival_2.44-1.1 iterators_1.0.12 glue_1.3.1
[37] registry_0.5-1 gtable_0.3.0 zlibbioc_1.28.0 XVector_0.22.0 Rgraphviz_2.26.0 scales_1.0.0
[43] pheatmap_1.0.12 DBI_1.0.0 rngtools_1.4 bibtex_0.4.2 ggthemes_4.2.0 Rcpp_1.0.2
[49] xtable_1.8-4 progress_1.2.2 htmlTable_1.13.2 foreign_0.8-72 bit_1.1-14 Formula_1.2-3
[55] DT_0.9 AnnotationForge_1.24.0 htmlwidgets_1.3 httr_1.4.1 threejs_0.3.1 RColorBrewer_1.1-2
[61] shinyAce_0.4.1 acepack_1.4.1 pkgconfig_2.0.3 XML_3.98-1.20 nnet_7.3-12 locfit_1.5-9.1
[67] labeling_0.3 tidyselect_0.2.5 rlang_0.4.0 later_0.8.0 munsell_0.5.0 tools_3.5.2
[73] RSQLite_2.1.2 evaluate_0.14 shinyBS_0.61 stringr_1.4.0 ggdendro_0.1-20 yaml_2.2.0
[79] knitr_1.25 bit64_0.9-7 PoiClaClu_1.0.2.1 purrr_0.3.2 RBGL_1.58.2 mime_0.7
[85] compiler_3.5.2 rstudioapi_0.10 curl_4.2 png_0.1-7 tibble_2.1.3 geneplotter_1.60.0
[91] stringi_1.4.3 ProtGenerics_1.14.0 Matrix_1.2-17 markdown_1.1 ggsci_2.9 vctrs_0.2.0
[97] pillar_1.4.2 BiocManager_1.30.4 d3heatmap_0.6.1.2 data.table_1.12.2 bitops_1.0-6 httpuv_1.5.2
[103] rtracklayer_1.42.2 R6_2.4.0 latticeExtra_0.6-28 promises_1.0.1 gridExtra_2.3 codetools_0.2-16
[109] MASS_7.3-51.4 assertthat_0.2.1 Category_2.48.1 pkgmaker_0.27 withr_2.1.2 GenomicAlignments_1.18.1 [115] Rsamtools_1.34.1 GenomeInfoDbData_1.2.0 hms_0.5.1 grid_3.5.2 rpart_4.1-15 tidyr_1.0.0
[121] rmarkdown_1.15 base64enc_0.1-3 `

[federicomarini]

Ok I might have an idea. You're using R 3.5.2 so it is not the latest from Bioc (in release, as we speak, it is 2.10.1). This conflicts with shinyAce >= 0.4.0.

Possible solutions: update R, and the Bioconductor version will be the latest. Or, install the devel version from github (remotes::install_github("federicomarini/pcaExplorer")). I'd put 2 cents that either would work. Safest would be the 1st for the obvious reason of keeping the whole Bioc installation "synced"

[devang-mehta]

The first option (re-installing R and all the packages) worked. Thanks for all the help and developing this very useful package!

[federicomarini]

You're very welcome!