The data is not in the file that it should be
1
0
Entering edit mode
@bioinformatics-10931
Last seen 2.4 years ago
United States

I am trying to run the script provided for this package
unfortunately, it gives an error,
I am using windows to run this


data(hyperLOPIT2015)
Warning message:
In data(hyperLOPIT2015) : data set ‘hyperLOPIT2015’ not found

 

FYI

> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:
[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] pRolocGUI_1.10.0     pRoloc_1.16.1        MLInterfaces_1.56.0  cluster_2.0.6        annotate_1.54.0     
 [6] XML_3.98-1.7         AnnotationDbi_1.38.1 IRanges_2.10.2       S4Vectors_0.14.3     MSnbase_2.2.0       
[11] ProtGenerics_1.8.0   BiocParallel_1.10.1  mzR_2.10.0           Rcpp_0.12.11         Biobase_2.36.2      
[16] BiocGenerics_0.22.0  BiocInstaller_1.26.0 limma_3.32.2         ggplot2_2.2.1        reshape2_1.4.2      
[21] data.table_1.10.4    hash_2.2.6          

loaded via a namespace (and not attached):
  [1] minqa_1.2.4           colorspace_1.3-2      hwriter_1.3.2         class_7.3-14          modeltools_0.2-21    
  [6] mclust_5.3            pls_2.6-0             base64enc_0.1-3       proxy_0.4-17          hexbin_1.27.1        
 [11] MatrixModels_0.4-1    affyio_1.46.0         DT_0.2                flexmix_2.3-14        mvtnorm_1.0-6        
 [16] codetools_0.2-15      splines_3.4.0         doParallel_1.0.10     impute_1.50.1         robustbase_0.92-7    
 [21] knitr_1.16            jsonlite_1.5          nloptr_1.0.4          caret_6.0-76          pbkrtest_0.4-7       
 [26] rda_1.0.2-2           kernlab_0.9-25        vsn_3.44.0            sfsmisc_1.1-1         shiny_1.0.3          
 [31] compiler_3.4.0        sampling_2.8          assertthat_0.2.0      Matrix_1.2-9          lazyeval_0.2.0       
 [36] htmltools_0.3.6       quantreg_5.33         tools_3.4.0           ggvis_0.4.3           gtable_0.2.0         
 [41] glue_1.0.0            affy_1.54.0           dplyr_0.7.0           MALDIquant_1.16.2     trimcluster_0.1-2    
 [46] gdata_2.18.0          preprocessCore_1.38.1 nlme_3.1-131          iterators_1.0.8       fpc_2.1-10           
 [51] stringr_1.2.0         lme4_1.1-13           lpSolve_5.6.13        mime_0.5              gtools_3.5.0         
 [56] dendextend_1.5.2      DEoptimR_1.0-8        zlibbioc_1.22.0       MASS_7.3-47           scales_0.4.1         
 [61] pcaMethods_1.68.0     SparseM_1.77          RColorBrewer_1.1-2    memoise_1.1.0         gridExtra_2.2.1      
 [66] biomaRt_2.32.1        rpart_4.1-11          stringi_1.1.5         RSQLite_1.1-2         genefilter_1.58.1    
 [71] randomForest_4.6-12   foreach_1.4.3         e1071_1.6-8           rlang_0.1.1           prabclus_2.2-6       
 [76] bitops_1.0-6          mzID_1.14.0           lattice_0.20-35       htmlwidgets_0.8       labeling_0.3         
 [81] gbm_2.1.3             plyr_1.8.4            magrittr_1.5          R6_2.2.1              DBI_0.6-1            
 [86] whisker_0.3-2         mgcv_1.8-17           survival_2.41-3       RCurl_1.95-4.8        nnet_7.3-12          
 [91] tibble_1.3.3          car_2.1-4             mlbench_2.1-1         viridis_0.4.0         grid_3.4.0           
 [96] FNN_1.1               ModelMetrics_1.1.0    threejs_0.2.2         digest_0.6.12         diptest_0.75-7       
[101] xtable_1.8-2          httpuv_1.3.3          munsell_0.4.3         viridisLite_0.2.0    
> 

 

 

 

pRolocGUI • 749 views
ADD COMMENT
1
Entering edit mode
@laurent-gatto-5645
Last seen 15 days ago
Belgium

The hyperLOPIT2015 data lives in the pRolocdata package, which you need to load first:

> library("pRolocdata")
> data(hyperLOPIT2015)
> hyperLOPIT2015
MSnSet (storageMode: lockedEnvironment)
assayData: 5032 features, 20 samples
  element names: exprs
protocolData: none
phenoData
  sampleNames: X126.rep1 X127N.rep1 ... X131.rep2 (20 total)
  varLabels: Replicate TMT.Reagent ... Iodixonal.Density (5 total)
  varMetadata: labelDescription
featureData
  featureNames: Q9JHU4 Q9QXS1-3 ... Q9Z2R6 (5032 total)
  fvarLabels: entry.name protein.description ... markers2015 (25 total)
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
Annotation:  
- - - Processing information - - -
Loaded on Mon Aug 22 13:47:10 2016.
Normalised to sum of intensities.
 MSnbase version: 1.21.7
ADD COMMENT

Login before adding your answer.

Traffic: 413 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6