Warning: Error in datatable: 'data' must be 2-dimensional (e.g. data frame or matrix)

[kamalmdmostafa]

When I try to run in locally, I always get the error warning at Motif enrichment step. However, when i use the same database, peptide modified sequence, and own background sequence it does not show any problem. The only problem about the online version is that, the server gets disconnected quiet often. Any solution to the local running of the MotifeRapp could help saving a lot of time.

Thanks in advance, Kamal

if(!require(motifeR)) devtools::install_github("wangshisheng/motifeRapp") Loading required package: motifeR library(motifeR) motifeR_app() Loading required package: shiny Need Shiny help? I'm available for consulting: http://attalitech.com

Attaching package: ‘shinyjs’

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gdata: Unable to locate valid perl interpreter gdata: gdata: read.xls() will be unable to read Excel XLS and XLSX files unless the 'perl=' argument is gdata: used to specify the location of a valid perl intrpreter. gdata: gdata: (To avoid display of this message in the future, please ensure perl is installed and gdata: available on the executable search path.) gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLX' (Excel 97-2004) files.

gdata: Unable to load perl libaries needed by read.xls() gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()' gdata: to automatically download and install the perl gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: ‘gdata’

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data.table 1.12.8 using 2 threads (see ?getDTthreads). Latest news: r-datatable.com

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Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

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Loading required package: S4Vectors Loading required package: stats4

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Loading required package: XVector

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Listening on http://0.0.0.0:3284 List of 2 $ Enrich.seq: list() $ Enrich.pro: list() Warning: Error in datatable: 'data' must be 2-dimensional (e.g. data frame or matrix) 105: stop 104: datatable 103: exprFunc [H:\R\R-3.6.2\library\motifeR\motifeRapp/app.R#1216] 102: widgetFunc 101: func 88: origRenderFunc 87: renderFunc 83: origRenderFunc 82: output$motiffuji 2: shiny::runApp 1: motifeR_app Warning: Error in [: incorrect number of dimensions 132: [H:\R\R-3.6.2\library\motifeR\motifeRapp/app.R#1148] 116: motiffujiout2 103: exprFunc [H:\R\R-3.6.2\library\motifeR\motifeRapp/app.R#1226] 102: widgetFunc 101: func 88: origRenderFunc 87: renderFunc 83: origRenderFunc 82: output$motiffuji2 2: shiny::runApp 1: motifeR_app

sessionInfo() R version 3.6.2 (2019-12-12) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64 (build 18362)

Matrix products: default

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

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

other attached packages: [1] rmotifx_1.0 stringr_1.4.0 stringi_1.4.3 Biostrings_2.54.0 XVector_0.26.0
[6] IRanges_2.20.1 S4Vectors_0.24.1 BiocGenerics_0.32.0 data.table_1.12.8 DT_0.11
[11] ggsci_2.9 gdata_2.18.0 openxlsx_4.1.4 shinyBS_0.61 shinyjs_1.0
[16] shiny_1.4.0 motifeR_0.2.1

loaded via a namespace (and not attached): [1] Rcpp_1.0.3 prettyunits_1.0.2 ps_1.3.0 gtools_3.8.1 assertthat_0.2.1
[6] rprojroot_1.3-2 digest_0.6.23 mime_0.8 R6_2.4.1 backports_1.1.5
[11] ggplot2_3.2.1 pillar_1.4.3 zlibbioc_1.32.0 rlang_0.4.2 lazyeval_0.2.2
[16] curl_4.3 rstudioapi_0.10 callr_3.4.0 htmlwidgets_1.5.1 munsell_0.5.0
[21] compiler_3.6.2 httpuv_1.5.2 pkgconfig_2.0.3 pkgbuild_1.0.6 htmltools_0.4.0
[26] tidyselect_0.2.5 tibble_2.1.3 fansi_0.4.1 crayon_1.3.4 dplyr_0.8.3
[31] withr_2.1.2 later_1.0.0 grid_3.6.2 jsonlite_1.6 xtable_1.8-4
[36] gtable_0.3.0 lifecycle_0.1.0 magrittr_1.5 scales_1.1.0 zip_2.0.4
[41] cli_2.0.1 promises_1.1.0 remotes_2.1.0 tools_3.6.2 glue_1.3.1
[46] purrr_0.3.3 crosstalk_1.0.0 processx_3.4.1 fastmap_1.0.1 yaml_2.2.0
[51] colorspace_1.4-1 BiocManager_1.30.10

[wangshisheng]

Hi Kamal,

Could you provide some detailed information, such as the screenshot of the error and the parameters? If so, I may give some effective help. I guess you don't prepare your data right or set the parameters well.

Shisheng

[kamalmdmostafa]

Hi Shisheng, Thank you so much for your kind response.

I have attached the screenshots from the installation to the final error here. I hope it makes clear to you. Or if you need i can provide my raw sample data with database FASTA and background sequences.

Best regards, Kamal

P.S. the images are in chronological order. Installation Data import Pre-alignment

Own background upload

Motif Enrichment on the way

Error

[wangshisheng]

Hi Kamal,

I suggest you should read the manual first, it is easy actually. I find some basic improper parameter setting, for example:

1. The 'Label of modification' in the parameter is '#', while those in your peptide list are '@'. Therefore, I suggest you change your '@' to '#' in your peptide list.

2. You have uploaded your fasta file in the 'Import Data' part, so you need not import again in the 'Own Background' part, just skip this step.

You can try it again as what I say above, if this error still exists, you can send your raw sample data with database FASTA to me.

Bests, Shisheng

[kamalmdmostafa]

Hi Shisheng,

Actually that was a wrong screenshot I took before. I updated the screenshots where I used the modification using '#' instead of '@'.

I am sending you the raw sample data with my Fasta database at your outlook 'wssdandan2009@outlook.com' email.

Thanks again.

Kamal

[wangshisheng]

Hi Kamal,

You can check and download the attached file, in which I processed your data and paste the detailed parameters and results. Help_Kamal_20200110.pptx

You can try it by yourself~~Hope hearing good news from you^_^

Bests, Shisheng

[kamalmdmostafa]

Hi Shisheng,

Thanks again. I figured out the problem. I have been using the original r-motifx for a while; after installing your modified rmotifx_1.0, things started to go in the right direction.

Kudos to your help.

Bests, Kamal