[R] Error in GDCprepare step of TCGAbiolinks
Ankita Lawarde
lawarde.ankita1 at gmail.com
Wed Mar 21 08:01:05 CET 2018
Dear Sir/ma'am,
I'm using R-3.4.4 and TCGAbiolinks package for the analysis of GDC data.
Till today i have reintalled R and R studio for 5 times but one error comes
when i analyze the GDC data at the step GDCprepare. the data i am using is
not a legacy data of GDC data portal.
I think the problem is with my Laptop only because i have run the same
commands in another PC and there was no error. Thus i have uninstalled and
again installed the R but the error is not going.
Today i have installed the developer version of TCGAbiolinks. and the error
is still there.
I have attached the code used and the session info.
Every time i run this GDCprepare command this same error comes as biomart
service is not available. So i had contaced the Biomart people but they
said that the Biomart is working fine.
below is the complete R code i am usign with the corresponding error,
library(TCGAbiolinks)
query.exp <- GDCquery(project = "TCGA-LUAD",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "HTSeq - Counts",
experimental.strategy = "RNA-Seq")
query_load <- GDCdownload(query.exp)
luad.exp <- GDCprepare(query = query.exp, save = TRUE, save.filename =
"TCGA_LUAD_Exp.rda",
summarizedExperiment = TRUE)
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Starting to add information to samples
=> Add clinical information to samples
Add FFPE information. More information at:
=> https://cancergenome.nih.gov/cancersselected/biospeccriteria
=>
http://gdac.broadinstitute.org/runs/sampleReports/latest/FPPP_FFPE_Cases.html
=> Adding subtype information to samples
luad subtype information from:doi:10.1038/nature13385
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://www.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt
Request to BioMart web service failed.
The BioMart web service you're accessing may be down.
Check the following URL and see if this website is available:
http://uswest.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt&redirect=no
Error: $ operator is invalid for atomic vectors
sessionInfo()
R version 3.4.4 (2018-03-15)
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
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
methods base
other attached packages:
[1] TCGAbiolinks_2.7.21 SummarizedExperiment_1.8.1
DelayedArray_0.4.1 matrixStats_0.53.1
[5] Biobase_2.38.0 GenomicRanges_1.30.0
GenomeInfoDb_1.14.0 IRanges_2.12.0
[9] S4Vectors_0.16.0 BiocGenerics_0.24.0
RColorBrewer_1.1-2 edgeR_3.20.9
[13] limma_3.34.9
loaded via a namespace (and not attached):
[1] colorspace_1.3-2 selectr_0.3-2 rjson_0.2.15
[4] hwriter_1.3.2 circlize_0.4.3
XVector_0.18.0
[7] GlobalOptions_0.0.13 ggpubr_0.1.6 matlab_1.0.2
[10] ggrepel_0.7.0 bit64_0.9-7
AnnotationDbi_1.40.0
[13] xml2_1.2.0 codetools_0.2-15
splines_3.4.4
[16] R.methodsS3_1.7.1 mnormt_1.5-5
doParallel_1.0.11
[19] DESeq_1.30.0 geneplotter_1.56.0 knitr_1.20
[22] jsonlite_1.5 Rsamtools_1.30.0 km.ci_0.5-2
[25] broom_0.4.3 annotate_1.56.1
cluster_2.0.6
[28] R.oo_1.21.0 readr_1.1.1
compiler_3.4.4
[31] httr_1.3.1 assertthat_0.2.0
Matrix_1.2-12
[34] lazyeval_0.2.1 prettyunits_1.0.2 tools_3.4.4
[37] bindrcpp_0.2 gtable_0.2.0 glue_1.2.0
[40] GenomeInfoDbData_1.0.0 reshape2_1.4.3 dplyr_0.7.4
[43] ggthemes_3.4.0 ShortRead_1.36.1 Rcpp_0.12.16
[46] Biostrings_2.46.0 nlme_3.1-131.1
rtracklayer_1.38.3
[49] iterators_1.0.9 psych_1.7.8
stringr_1.3.0
[52] rvest_0.3.2 XML_3.98-1.10 zoo_1.8-1
[55] zlibbioc_1.24.0 scales_0.5.0
aroma.light_3.8.0
[58] hms_0.4.2 curl_3.1
ComplexHeatmap_1.17.1
[61] memoise_1.1.0 gridExtra_2.3 KMsurv_0.1-5
[64] ggplot2_2.2.1 downloader_0.4
biomaRt_2.34.2
[67] latticeExtra_0.6-28 stringi_1.1.7 RSQLite_2.0
[70] genefilter_1.60.0 foreach_1.4.4
RMySQL_0.10.14
[73] GenomicFeatures_1.30.3 BiocParallel_1.12.0 shape_1.4.4
[76] rlang_0.2.0 pkgconfig_2.0.1 bitops_1.0-6
[79] lattice_0.20-35 purrr_0.2.4 bindr_0.1.1
[82] GenomicAlignments_1.14.1 cmprsk_2.2-7 bit_1.1-12
[85] plyr_1.8.4 magrittr_1.5 R6_2.2.2
[88] DBI_0.8 mgcv_1.8-23 pillar_1.2.1
[91] foreign_0.8-69 survival_2.41-3
RCurl_1.95-4.10
[94] tibble_1.4.2 EDASeq_2.12.0
survMisc_0.5.4
[97] GetoptLong_0.1.6 progress_1.1.2
locfit_1.5-9.1
[100] grid_3.4.4 sva_3.26.0
data.table_1.10.4-3
[103] blob_1.1.0 ConsensusClusterPlus_1.42.0
digest_0.6.15
[106] xtable_1.8-2 tidyr_0.8.0
R.utils_2.6.0
[109] munsell_0.4.3 survminer_0.4.2
I hope this helps to understand my problem.
I look forward to hear from you
Regards,
Ankita
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