Data type error
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Entering edit mode
@mukhamadeevar-10991
Last seen 7.3 years ago

Hi,

 

I have a data type error when using GDCquery:

query_normal <- GDCquery(project = "TCGA-ACC", data.category = "Gene expression", data.type = "Gene expression quantification", platform = "Illumina HiSeq", file.type = "normalized_results", sample.type = "Solid Tissue Normal", legacy = TRUE)
Accessing GDC. This might take a while...
Error in GDCquery(project = "TCGA-ACC", data.category = "Gene expression",  : 
  Please set a valid data.type argument from the list below:
  => 

And there is no list that shows valid data types.

I checked it on GDC portal that such data type exists in data category "Gene expression" and the data is open.

Please, can you tell what to do to get such data using TCGAbiolinks.

Thank you!

Session Info:

R version 3.3.1 (2016-06-21)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=Russian_Russia.1251  LC_CTYPE=Russian_Russia.1251   
[3] LC_MONETARY=Russian_Russia.1251 LC_NUMERIC=C                   
[5] LC_TIME=Russian_Russia.1251    

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

other attached packages:
[1] TCGAbiolinks_2.0.13        SummarizedExperiment_1.2.3 Biobase_2.32.0            
[4] GenomicRanges_1.24.2       GenomeInfoDb_1.8.3         IRanges_2.6.1             
[7] S4Vectors_0.10.3           BiocGenerics_0.18.0       

loaded via a namespace (and not attached):
  [1] TH.data_1.0-7                           colorspace_1.3-1                       
  [3] rjson_0.2.15                            hwriter_1.3.2                          
  [5] class_7.3-14                            modeltools_0.2-21                      
  [7] mclust_5.2                              circlize_0.3.9                         
  [9] XVector_0.12.1                          GlobalOptions_0.0.10                   
 [11] parmigene_1.0.2                         matlab_1.0.2                           
 [13] hexbin_1.27.1                           affyio_1.42.0                          
 [15] ggrepel_0.6.3                           flexmix_2.3-13                         
 [17] AnnotationDbi_1.34.4                    mvtnorm_1.0-5                          
 [19] xml2_1.0.0                              coin_1.1-2                             
 [21] codetools_0.2-15                        splines_3.3.1                          
 [23] R.methodsS3_1.7.1                       doParallel_1.0.10                      
 [25] DESeq_1.24.0                            robustbase_0.92-6                      
 [27] knitr_1.15                              geneplotter_1.50.0                     
 [29] jsonlite_1.1                            Rsamtools_1.24.0                       
 [31] annotate_1.50.1                         cluster_2.0.5                          
 [33] kernlab_0.9-25                          R.oo_1.21.0                            
 [35] supraHex_1.10.0                         graph_1.50.0                           
 [37] readr_1.0.0                             httr_1.2.1                             
 [39] assertthat_0.1                          Matrix_1.2-7.1                         
 [41] lazyeval_0.2.0                          TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [43] limma_3.28.21                           tools_3.3.1                            
 [45] igraph_1.0.1                            gtable_0.2.0                           
 [47] affy_1.50.0                             dplyr_0.5.0                            
 [49] ggthemes_3.2.0                          ShortRead_1.30.0                       
 [51] Rcpp_0.12.8                             trimcluster_0.1-2                      
 [53] Biostrings_2.40.2                       gdata_2.17.0                           
 [55] ape_3.5                                 preprocessCore_1.34.0                  
 [57] nlme_3.1-128                            rtracklayer_1.32.2                     
 [59] iterators_1.0.8                         fpc_2.1-10                             
 [61] stringr_1.1.0                           rvest_0.3.2                            
 [63] gtools_3.5.0                            XML_3.98-1.5                           
 [65] dendextend_1.3.0                        edgeR_3.14.0                           
 [67] DEoptimR_1.0-8                          zlibbioc_1.18.0                        
 [69] MASS_7.3-45                             zoo_1.7-13                             
 [71] scales_0.4.1                            aroma.light_3.2.0                      
 [73] BiocInstaller_1.22.3                    sandwich_2.3-4                         
 [75] RColorBrewer_1.1-2                      curl_2.2                               
 [77] ComplexHeatmap_1.10.2                   ggplot2_2.2.0                          
 [79] downloader_0.4                          biomaRt_2.28.0                         
 [81] reshape_0.8.6                           latticeExtra_0.6-28                    
 [83] stringi_1.1.2                           RSQLite_1.0.0                          
 [85] highr_0.6                               genefilter_1.54.2                      
 [87] foreach_1.4.3                           caTools_1.17.1                         
 [89] GenomicFeatures_1.24.5                  BiocParallel_1.6.6                     
 [91] shape_1.4.2                             chron_2.3-47                           
 [93] prabclus_2.2-6                          matrixStats_0.51.0                     
 [95] bitops_1.0-6                            dnet_1.0.9                             
 [97] lattice_0.20-34                         GenomicAlignments_1.8.4                
 [99] GGally_1.3.0                            plyr_1.8.4                             
[101] magrittr_1.5                            R6_2.2.0                               
[103] gplots_3.0.1                            multcomp_1.4-6                         
[105] DBI_0.5-1                               whisker_0.3-2                          
[107] survival_2.40-1                         RCurl_1.95-4.8                         
[109] nnet_7.3-12                             tibble_1.2                             
[111] EDASeq_2.6.2                            KernSmooth_2.23-15                     
[113] GetoptLong_0.1.5                        grid_3.3.1                             
[115] data.table_1.9.6                        Rgraphviz_2.16.0                       
[117] ConsensusClusterPlus_1.36.0             digest_0.6.10                          
[119] diptest_0.75-7                          xtable_1.8-2                           
[121] R.utils_2.5.0                           munsell_0.4.3  
tcgabiolinks • 791 views
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0
Entering edit mode
@tiago-chedraoui-silva-8877
Last seen 3.6 years ago
Brazil - University of São Paulo/ Los A…

Hi, there is no Solid Tissue Normal samples for your search. I just fixed the error message.

Best regards,

Tiago

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