User: sabarinath.chandrasekharan

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Posts by sabarinath.chandrasekharan

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Comment: C: TCGAbiolinks GDCprepare fails to connect to Biomart web server
... Sorry this code also does not work. > hg19 <- get.GRCh.bioMart() Downloading genome information. Using: Homo sapiens genes (GRCh37.p13) Show Traceback Rerun with Debug Error in value[[3L]](cond) : Request to BioMart web service failed. Verify if you are still connected to the interne ...
written 2.5 years ago by sabarinath.chandrasekharan10
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Comment: C: TCGAbiolinks GDCprepare fails to connect to Biomart web server
... Sorry about the delay:  Here is the SessionInfo as well > query_GBM <- GDCquery(project = "TCGA-GBM", + data.category = "Gene expression", + data.type = "Gene expression quantification", + platform = "Illumina HiSeq", file.type = "norma ...
written 2.5 years ago by sabarinath.chandrasekharan10
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Answer: A: TCGAbiolinks GDCprepare fails to connect to Biomart web server
... I am still having this problem of GDCprepare not being able to connecto Biomart server, while other programs can. anybody else is facing this problem? Is there any work around? ...
written 2.6 years ago by sabarinath.chandrasekharan10
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Answer: A: TCGAbiolinks GDCprepare fails to connect to Biomart web server
... GDCprepare throwed a different error when I tried with a different data set > query <- GDCquery(project = "TCGA-LUSC", data.category = "Gene expression", data.type = "Gene Expression Quantification", platform = "Illumina HiSeq", file.type = "normalized_results", experimental.strategy = "RNA ...
written 2.6 years ago by sabarinath.chandrasekharan10
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Comment: C: TCGAbiolinks GDCprepare fails to connect to Biomart web server
... Still no luck. > grch37 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="grch37.ensembl.org", path="/biomart/martservice", dataset="hsapiens_gene_ensembl") > ensembl_75 = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="feb2014.archive.ensembl.org", path="/biomart/martservice", dataset="hsapiens ...
written 2.6 years ago by sabarinath.chandrasekharan10
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TCGAbiolinks GDCprepare fails to connect to Biomart web server
... Hi,   I am trying to work with TCGAbiolinks, but am having problem with GDCprepare. It fails to connect to BioMart web service.    ​queryGBM <- GDCquery(project = "TCGA-GBM", + data.category = "Gene expression", + data.type = "Gene expression quantificatio ...
tcgabiolinks gdcprepare written 2.6 years ago by sabarinath.chandrasekharan10
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Comment: C: Errors in TCGAbiolinks
... Hi, the GDCquery is now working as it should, but GDCdownload  is downloading only a partial file. Note: I am behind a university proxy, could it be due to this?  > query <- GDCquery(project = "TCGA-ACC", data.category = "Copy Number Variation", + data.type = "Copy Number ...
written 2.7 years ago by sabarinath.chandrasekharan10
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Comment: C: Errors in TCGAbiolinks
... Hi, I tried the github version, but that also is throwing an error   > query <- GDCquery(project = "TARGET-AML", + data.category = "Transcriptome Profiling", + data.type = "Gene Expression Quantification", + workflow.type = "HTSeq - Cou ...
written 2.7 years ago by sabarinath.chandrasekharan10
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Comment: C: Errors in TCGAbiolinks
... Thank you very much for your support! ...
written 2.7 years ago by sabarinath.chandrasekharan10
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Errors in TCGAbiolinks
... Hi,  I am having trouble with two modules of TCGAbiolinks (re-installed yesterday)  1. GDCdownload and 2. GDCquery_Maf   GDCdownload gives the following error, whenever used > query <- GDCquery(project = "TARGET-AML", + data.category = "Transcriptome Profiling", + ...
tcgabiolinks written 2.7 years ago by sabarinath.chandrasekharan10 • updated 2.7 years ago by Tiago Chedraoui Silva190

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