Question: TCGAbiolinks XML error
1
gravatar for Markus List
2.4 years ago by
Markus List20
Freising
Markus List20 wrote:

Some code that worked perfectly fine in Bioconductor 3.4 is not working any longer. It looks like the code for implementing clinical data seems broken. It there a fix / workaround available?

 

library(TCGAbiolinks)
library(SummarizedExperiment)

query <- GDCquery(project = "TCGA-LIHC",
                  data.category = "Gene expression",
                  data.type = "Gene expression quantification",
                  experimental.strategy = "RNA-Seq",
                  platform = "Illumina HiSeq",
                  file.type = "normalized_results",
                  legacy = TRUE)

GDCdownload(query)
LIHC_gene_assay <- GDCprepare(query)
 |=================================================================================================================| 100%
Downloading genome information (try:0) Using: Homo sapiens genes (GRCh37.p13)
Loading from disk
Starting to add information to samples
=> Add clinical information to samples
Error: lexical error: invalid char in json text.
                                       <?xml version="1.0" ?> <respons
                     (right here) ------^

 

sessionInfo()

 

R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

Matrix products: default
BLAS: /usr/lib/atlas-base/atlas/libblas.so.3.0
LAPACK: /usr/lib/atlas-base/atlas/liblapack.so.3.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
 [1] tidyr_0.6.3                dplyr_0.7.1                SummarizedExperiment_1.6.3 DelayedArray_0.2.7        
 [5] matrixStats_0.52.2         Biobase_2.36.2             GenomicRanges_1.28.3       GenomeInfoDb_1.12.2       
 [9] IRanges_2.10.2             S4Vectors_0.14.3           BiocGenerics_0.22.0        TCGAbiolinks_2.4.3   

 

tcgabiolinks • 388 views
ADD COMMENTlink modified 2.2 years ago by lqfuture0 • written 2.4 years ago by Markus List20
Answer: TCGAbiolinks XML error
0
gravatar for lqfuture
2.2 years ago by
lqfuture0
lqfuture0 wrote:

Hi, I meet the same problem with you.

ADD COMMENTlink written 2.2 years ago by lqfuture0
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