Entering edit mode
Mariana Boroni
▴
10
@mariana-boroni-5838
Last seen 7.5 years ago
Hi all, I am facing a problem with TCGAbiolinks, when I'm using the GDCprepare command:
This is what I ma doing:
library("TCGAbiolinks")
library("ComplexHeatmap")
library("SummarizedExperiment")
# Download the expression data
query.exp <- GDCquery(project = c("TCGA-ESCA"),
legacy = TRUE,
data.category = "Gene expression",
data.type = "Gene expression quantification",
platform = "Illumina HiSeq",
file.type = "results")
GDCdownload(query.exp)
> ESCA.exp <- GDCprepare(query = query.exp, save = TRUE, save.filename = "ESCA_Exp.rda")
|===============================================================================================================================| 100%Extra content at the end of the document
Error: 1: Extra content at the end of the document
Any idea what could be wrong and if there is a way to fix it? Appreciate any help or suggestions.
Here's my session info:
> sessionInfo()
R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 16.04.1 LTS locale: [1] LC_CTYPE=pt_BR.UTF-8 LC_NUMERIC=C LC_TIME=pt_BR.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=pt_BR.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=pt_BR.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=pt_BR.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats4 parallel grid stats graphics grDevices utils datasets methods base other attached packages: [1] SummarizedExperiment_1.0.2 Biobase_2.30.0 GenomicRanges_1.22.4 GenomeInfoDb_1.6.3 [5] IRanges_2.4.8 S4Vectors_0.8.11 BiocGenerics_0.16.1 ComplexHeatmap_1.10.2 [9] TCGAbiolinks_2.1.6 loaded via a namespace (and not attached): [1] circlize_0.3.8 aroma.light_3.0.0 plyr_1.8.4 [4] igraph_1.0.1 lazyeval_0.2.0 ConsensusClusterPlus_1.24.0 [7] splines_3.2.3 BiocParallel_1.4.3 ggplot2_2.1.0 [10] TH.data_1.0-7 digest_0.6.10 foreach_1.4.3 [13] BiocInstaller_1.20.3 gdata_2.17.0 magrittr_1.5 [16] cluster_2.0.4 doParallel_1.0.10 limma_3.26.9 [19] Biostrings_2.38.4 readr_1.0.0 annotate_1.48.0 [22] matrixStats_0.50.2 R.utils_2.3.0 sandwich_2.3-4 [25] colorspace_1.2-6 rvest_0.3.2 ggrepel_0.5 [28] haven_0.2.1 dplyr_0.5.0 jsonlite_1.0 [31] RCurl_1.95-4.8 hexbin_1.27.1 TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2 [34] graph_1.48.0 genefilter_1.52.1 lme4_1.1-12 [37] supraHex_1.8.0 survival_2.39-5 zoo_1.7-13 [40] iterators_1.0.8 ape_3.5 gtable_0.2.0 [43] zlibbioc_1.16.0 XVector_0.10.0 sjstats_0.4.0 [46] GetoptLong_0.1.4 sjmisc_1.8 kernlab_0.9-24 [49] Rgraphviz_2.14.0 shape_1.4.2 prabclus_2.2-6 [52] DEoptimR_1.0-6 scales_0.4.0 DESeq_1.22.1 [55] futile.options_1.0.0 mvtnorm_1.0-5 DBI_0.5 [58] GGally_1.2.0 edgeR_3.12.1 ggthemes_3.2.0 [61] Rcpp_0.12.6 xtable_1.8-2 matlab_1.0.2 [64] mclust_5.2 preprocessCore_1.32.0 httr_1.2.1 [67] gplots_3.0.1 RColorBrewer_1.1-2 fpc_2.1-10 [70] modeltools_0.2-21 reshape_0.8.5 XML_3.98-1.4 [73] R.methodsS3_1.7.1 flexmix_2.3-13 nnet_7.3-12 [76] reshape2_1.4.1 AnnotationDbi_1.32.3 munsell_0.4.3 [79] tools_3.2.3 downloader_0.4 RSQLite_1.0.0 [82] broom_0.4.1 stringr_1.1.0 knitr_1.14 [85] robustbase_0.92-6 caTools_1.17.1 dendextend_1.3.0 [88] coin_1.1-2 EDASeq_2.4.1 nlme_3.1-128 [91] whisker_0.3-2 R.oo_1.20.0 xml2_1.0.0 [94] biomaRt_2.26.1 curl_1.2 affyio_1.40.0 [97] tibble_1.2 geneplotter_1.48.0 stringi_1.1.1 [100] futile.logger_1.4.3 GenomicFeatures_1.22.13 lattice_0.20-33 [103] trimcluster_0.1-2 Matrix_1.2-7 psych_1.6.6 [106] nloptr_1.0.4 effects_3.1-1 stringdist_0.9.4.1 [109] GlobalOptions_0.0.10 data.table_1.9.6 cowplot_0.6.2 [112] bitops_1.0-6 dnet_1.0.9 rtracklayer_1.30.4 [115] R6_2.1.3 latticeExtra_0.6-28 affy_1.48.0 [118] hwriter_1.3.2 ShortRead_1.28.0 KernSmooth_2.23-15 [121] codetools_0.2-14 lambda.r_1.1.9 MASS_7.3-45 [124] gtools_3.5.0 assertthat_0.1 chron_2.3-47 [127] rjson_0.2.15 mnormt_1.5-4 GenomicAlignments_1.6.3 [130] Rsamtools_1.22.0 multcomp_1.4-6 diptest_0.75-7 [133] sjPlot_2.0.2 tidyr_0.6.0 class_7.3-14 [136] minqa_1.2.4
Sincerely,
Mariana
