I'm using LUAD data from FireBrowse and i was following RTCGAToolbox tutorial (http://genomicsclass.github.io/book/pages/tcga.html) but when try to download the data i'm getting one error,
Here is the R code i used ,
library(RTCGAToolbox) readData = getFirehoseData (dataset="LUAD", runDate="20160128",forceDownload = TRUE, Mutation=TRUE, Methylation=TRUE, RNASeq2GeneNorm=TRUE)
And the error message is,
Error: failed to load external entity "http://gdac.broadinstitute.org/runs/stddata__2016_01_28/data/LUAD/20160128/"
I even tried to remove thr runDate option from the getFirehoseData, but it still gives the same error.
1) Can anyone know why is this error coming ?, and how to get rid og this error?
I read some notes from this links https://confluence.broadinstitute.org/display/GDAC/Standardized+Data+Run+Release+Notes
It says: Please use last month's RPPA data if you are analyzing LUAD, so i used rundate as 20170606 but still the error is there.
But i'm interested in only clinical data of LUAD. and not in RPPA data.
Any suggestion will really help me remove this query.
here is the session info,
> 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:  LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252  LC_MONETARY=English_United States.1252  LC_NUMERIC=C  LC_TIME=English_United States.1252 attached base packages:  stats graphics grDevices utils datasets methods base other attached packages:  devtools_1.13.5 RTCGAToolbox_2.8.0 loaded via a namespace (and not attached):  XVector_0.18.0 GenomicRanges_1.30.3  BiocGenerics_0.24.0 splines_3.4.4  zlibbioc_1.24.0 IRanges_2.12.0  lattice_0.20-35 R6_2.2.2  httr_1.3.1 GenomeInfoDb_1.14.0  tools_3.4.4 SummarizedExperiment_1.8.1  parallel_3.4.4 grid_3.4.4  Biobase_2.38.0 data.table_1.10.4-3  git2r_0.21.0 withr_2.1.2  matrixStats_0.53.1 digest_0.6.15  survival_2.41-3 RJSONIO_1.3-0  Matrix_1.2-12 GenomeInfoDbData_1.0.0  S4Vectors_0.16.0 bitops_1.0-6  curl_3.2 RCurl_1.95-4.10  memoise_1.1.0 DelayedArray_0.4.1  limma_3.34.9 compiler_3.4.4  RCircos_1.2.0 stats4_3.4.4  XML_3.98-1.10 jsonlite_1.5
Thank you in advance.
Hi Marcel Ramos,
Yes, I have windows OS on my laptop
and that is the reason i was getting the error.
Thank you so much for the response.