Unable to run example for pRolocVis aggregate function

[rdogra8]

Hi, I was trying to run the pRolocVis for my data to visualize the peptides after aggregating the peptides, but was thrown an error. Then i ran the example dataset given for the package in the documentation i.e. hyperLOPIT2015ms2psm but again encountered the same error, please see here:

Command:

data("hyperLOPIT2015ms2psm")
pRolocVis(hyperLOPIT2015ms2psm, app = "aggregate", fcol = "markers",
          groupBy = "Protein.Group.Accessions")

Error:

Error in (function (od, vd)  : 
  object and replacement value dimnames differ

Could you please suggest what can be done regarding this?

[lgatto]

Could you please add your session information.

[rdogra8]

sessionInfo() R version 4.3.1 (2023-06-16 ucrt) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 11 x64 (build 22631)

Matrix products: default

locale: [1] LC_COLLATE=English_India.utf8 LC_CTYPE=English_India.utf8 LC_MONETARY=English_India.utf8 LC_NUMERIC=C
[5] LC_TIME=English_India.utf8

time zone: Europe/Brussels tzcode source: internal

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

other attached packages: [1] pRolocGUI_2.12.0 pRolocdata_1.40.0 pRoloc_1.42.0 BiocParallel_1.36.0 MLInterfaces_1.82.0 cluster_2.1.6
[7] annotate_1.80.0 XML_3.99-0.17 AnnotationDbi_1.64.1 IRanges_2.36.0 MSnbase_2.28.1 ProtGenerics_1.34.0 [13] S4Vectors_0.40.2 mzR_2.36.0 Rcpp_1.0.12 Biobase_2.62.0 BiocGenerics_0.48.1

loaded via a namespace (and not attached): [1] later_1.3.2 splines_4.3.1 bitops_1.0-7 filelock_1.0.3
[5] tibble_3.2.1 hardhat_1.4.0 preprocessCore_1.64.0 pROC_1.18.5
[9] rpart_4.1.23 lifecycle_1.0.4 doParallel_1.0.17 globals_0.16.3
[13] lattice_0.22-6 MASS_7.3-60 dendextend_1.17.1 magrittr_2.0.3
[17] sass_0.4.9 limma_3.58.1 plotly_4.10.4 jquerylib_0.1.4
[21] httpuv_1.6.15 MsCoreUtils_1.14.1 DBI_1.2.3 RColorBrewer_1.1-3
[25] lubridate_1.9.3 abind_1.4-5 zlibbioc_1.48.2 GenomicRanges_1.54.1
[29] purrr_1.0.2 mixtools_2.0.0 RCurl_1.98-1.16 nnet_7.3-19
[33] rappdirs_0.3.3 ipred_0.9-14 lava_1.8.0 GenomeInfoDbData_1.2.11
[37] listenv_0.9.1 parallelly_1.37.1 ncdf4_1.22 codetools_0.2-20
[41] DelayedArray_0.28.0 DT_0.33 xml2_1.3.6 tidyselect_1.2.1
[45] viridis_0.6.5 shinyWidgets_0.8.6 matrixStats_1.3.0 BiocFileCache_2.10.2
[49] jsonlite_1.8.8 caret_6.0-94 e1071_1.7-14 survival_3.7-0
[53] iterators_1.0.14 foreach_1.5.2 segmented_2.1-0 tools_4.3.1
[57] progress_1.2.3 glue_1.7.0 prodlim_2024.06.25 gridExtra_2.3
[61] SparseArray_1.2.4 xfun_0.45 MatrixGenerics_1.14.0 GenomeInfoDb_1.38.8
[65] dplyr_1.1.4 shinydashboard_0.7.2 withr_3.0.0 BiocManager_1.30.23
[69] fastmap_1.2.0 fansi_1.0.6 shinyjs_2.1.0 digest_0.6.36
[73] mime_0.12 timechange_0.3.0 R6_2.5.1 colorspace_2.1-0
[77] gtools_3.9.5 lpSolve_5.6.20 biomaRt_2.58.2 RSQLite_2.3.7
[81] utf8_1.2.4 tidyr_1.3.1 generics_0.1.3 hexbin_1.28.3
[85] data.table_1.15.4 recipes_1.1.0 FNN_1.1.4 class_7.3-22
[89] prettyunits_1.2.0 httr_1.4.7 htmlwidgets_1.6.4 S4Arrays_1.2.1
[93] ModelMetrics_1.2.2.2 pkgconfig_2.0.3 gtable_0.3.5 timeDate_4032.109
[97] blob_1.2.4 impute_1.76.0 XVector_0.42.0 htmltools_0.5.8.1
[101] shinyhelper_0.3.2 MALDIquant_1.22.2 clue_0.3-65 scales_1.3.0
[105] png_0.1-8 gower_1.0.1 knitr_1.48 rstudioapi_0.16.0
[109] tzdb_0.4.0 reshape2_1.4.4 shinydashboardPlus_2.0.4 coda_0.19-4.1
[113] nlme_3.1-165 curl_5.2.1 proxy_0.4-27 cachem_1.1.0
[117] stringr_1.5.1 miniUI_0.1.1.1 parallel_4.3.1 mzID_1.40.0
[121] vsn_3.70.0 pillar_1.9.0 grid_4.3.1 vctrs_0.6.5
[125] pcaMethods_1.94.0 promises_1.3.0 randomForest_4.7-1.1 dbplyr_2.5.0
[129] xtable_1.8-4 readr_2.1.5 mvtnorm_1.2-5 cli_3.6.2
[133] compiler_4.3.1 rlang_1.1.4 crayon_1.5.3 future.apply_1.11.2
[137] LaplacesDemon_16.1.6 mclust_6.1.1 affy_1.80.0 plyr_1.8.9
[141] stringi_1.8.4 viridisLite_0.4.2 munsell_0.5.1 Biostrings_2.70.3
[145] lazyeval_0.2.2 colourpicker_1.3.0 Matrix_1.5-4.1 hms_1.1.3
[149] bit64_4.0.5 future_1.33.2 ggplot2_3.5.1 shiny_1.8.1.1
[153] KEGGREST_1.42.0 statmod_1.5.0 SummarizedExperiment_1.32.0 kernlab_0.9-32
[157] memoise_2.0.1 bslib_0.7.0 affyio_1.72.0 bit_4.0.5
[161] sampling_2.10

[lgatto]

@rdogra8 - could you install the package from github with

BiocManager::install("lgatto/pRolocGUI")

and try again. It should work now.

I'm closing the issue, but do reopen it if you still have the error.