Warning: Error in read.table: more columns than column names when uploading example datasets

[artur-sannikov]

Hello,

I'm trying to use the datasets from tables in your paper. I removed the first line with the table title as required.

I'm uploading Table S2 (microbiomics, ASV 16S):

1. Data type: omics data
2. Select Is microbime data
3. Use for single omics analysis
4. Name for plots "Microbiomics"
5. Hit Save

I then get this error:

Loading required package: shiny

Listening on http://127.0.0.1:6806
Warning: Error in read.table: more columns than column names
  3: runApp [/tmp/RtmpINwZEU/R.INSTALL8df4b4aba40ad/shiny/R/runapp.R#388]
  2: print.shiny.appobj [/tmp/RtmpINwZEU/R.INSTALL8df4b4aba40ad/shiny/R/shinyapp.R#565]
  1: <Anonymous>

I tried to open this file manually with read.table and read.csv:

asv_16s <- read.csv("microbiomics_asv_16s.csv")
asv_16s <- read.table("microbiomics_asv_16s.csv", header = TRUE)

and get the same error.

> sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 21.3

Matrix products: default
BLAS/LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so;  LAPACK version 3.10.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Helsinki
tzcode source: system (glibc)

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

other attached packages:
 [1] shiny_1.8.1.1                  
 [2] TreeSummarizedExperiment_2.10.0
 [3] Biostrings_2.70.3              
 [4] XVector_0.42.0                 
 [5] SingleCellExperiment_1.24.0    
 [6] MultiAssayExperiment_1.28.0    
 [7] SummarizedExperiment_1.32.0    
 [8] Biobase_2.62.0                 
 [9] GenomicRanges_1.54.1           
[10] GenomeInfoDb_1.38.8            
[11] IRanges_2.36.0                 
[12] S4Vectors_0.40.2               
[13] BiocGenerics_0.48.1            
[14] MatrixGenerics_1.14.0          
[15] matrixStats_1.2.0              
[16] BiocManager_1.30.22            

loaded via a namespace (and not attached):
 [1] tidyselect_1.2.1        golem_0.4.1            
 [3] dplyr_1.1.4             bitops_1.0-7           
 [5] fastmap_1.1.1           RCurl_1.98-1.14        
 [7] lazyeval_0.2.2          promises_1.3.0         
 [9] shinyjs_2.1.0           digest_0.6.35          
[11] mime_0.12               lifecycle_1.0.4        
[13] Holomics_1.1.0          tidytree_0.4.6         
[15] magrittr_2.0.3          compiler_4.3.2         
[17] rlang_1.1.3             config_0.3.2           
[19] sass_0.4.9              tools_4.3.2            
[21] utf8_1.2.4              yaml_2.3.8             
[23] knitr_1.46              S4Arrays_1.2.1         
[25] htmlwidgets_1.6.4       shinybusy_0.3.3        
[27] DelayedArray_0.28.0     abind_1.4-5            
[29] BiocParallel_1.36.0     purrr_1.0.2            
[31] shinyWidgets_0.8.4      grid_4.3.2             
[33] fansi_1.0.6             xtable_1.8-4           
[35] cli_3.6.2               crayon_1.5.2           
[37] treeio_1.26.0           generics_0.1.3         
[39] rstudioapi_0.16.0       commonmark_1.9.1       
[41] visNetwork_2.1.2        ape_5.7-1              
[43] cachem_1.0.8            zlibbioc_1.48.2        
[45] parallel_4.3.2          vctrs_0.6.5            
[47] yulab.utils_0.1.4       Matrix_1.6-1.1         
[49] jsonlite_1.8.8          tippy_0.1.0            
[51] crosstalk_1.2.1         attempt_0.3.1          
[53] fontawesome_0.5.2       jquerylib_0.1.4        
[55] tidyr_1.3.1             glue_1.7.0             
[57] codetools_0.2-19        DT_0.33                
[59] bs4Dash_2.3.3           later_1.3.2            
[61] tibble_3.2.1            pillar_1.9.0           
[63] htmltools_0.5.8.1       GenomeInfoDbData_1.2.11
[65] R6_2.5.1                lattice_0.21-9         
[67] markdown_1.12           memoise_2.0.1          
[69] renv_1.0.5              httpuv_1.6.15          
[71] bslib_0.7.0             Rcpp_1.0.12            
[73] SparseArray_1.2.4       nlme_3.1-163           
[75] shinyvalidate_0.1.3     xfun_0.43              
[77] fs_1.6.3                pkgconfig_2.0.3

I suspect it's because of the incorrect format for the csv files.

[kathi-munk]

Hello, thank you for bringing this up. There is an error in our published test data. We are currently trying to fix this and update our publication.

[kathi-munk]

The publication was updated with instructions on how to use the test data. Thanks again for bringing this up!