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rli012 / GDCRNATools

GDCRNATools: an R/Bioconductor package for integrative analysis of lncRNA, miRNA and mRNA data in GDC
Apache License 2.0
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Error while using gdcRNADownload() #3

Open VeronicaFung opened 6 years ago

VeronicaFung commented 6 years ago

I installed R-3.4.1 by Miniconda, and managed to installed the GDCRNATools, but while testing with your instruction to download RNA data (http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNATools/inst/doc/GDCRNATools.html#data-preparation), I got a error when using gdcRNADownload(). The error is like this:

default

and my sessionInfo() is below: 1 2 3

Do you have any idea why I got this problem and how to solve? Thank you so much!

Jialab-UCR commented 6 years ago

Hi, could you please try method='gdc-client', the api method sometimes doesn't work well. Thanks

VeronicaFung commented 6 years ago

Thank you, now I tried 'gdc-client', it works on my personal computer, but our host got some other problem. Seems the glibc is too old. Anyway, will find a way to solve that. Thank you so much for replying.

chenjy33 commented 6 years ago

The downloaded RNAseq or miRNA data by 'gdc-client' method in gdcRNADownload() were .htseq.counts.gz files in separate file folders. But the api method can directly get those .htseq.counts.gz files in the working path, which is important to run gdcRNAMerge(). Do you have any idea to solve the problem?