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getTCGA Error because of invalid 'description' argument #11

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nturaga opened this issue Jun 26, 2015 · 1 comment
Open

getTCGA Error because of invalid 'description' argument #11

nturaga opened this issue Jun 26, 2015 · 1 comment

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@nturaga
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nturaga commented Jun 26, 2015

x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-07-0227-20A-01D-A39G-05.txt
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56K-01A-32D-A39G-05.txt
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56L-01A-31D-A39G-05.txt
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56N-01A-12D-A39G-05.txt
x jhu-usc.edu_READ.HumanMethylation450.Level_3.7.3.0/MANIFEST.txt
Error in file(file, "rt") : invalid 'description' argument

The Error happened in both BLCA and READ. The MANIFEST file itself has missing DESCRIPTION tag

f8c19c7c93155778edc6bd169d808068  README_DCC.txt
a62a715e87ca3d21027aaa10567bf042  jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-07-0227-20A-01D-A39G-05.txt
0ac1003dfbab4a48bcc292630d8e314d  jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56K-01A-32D-A39G-05.txt
8addef41b4dc83c315d2812027d95769  jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56L-01A-31D-A39G-05.txt
7c86b5a7306b634aa8c50a9df5be98ee  jhu-usc.edu_READ.HumanMethylation450.7.lvl-3.TCGA-AF-A56N-01A-12D-A39G-05.txt
@nturaga nturaga changed the title getTCGA getTCGA Error because of invalid 'description' argument Jun 26, 2015
@tiagochst
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@nitesh1989 I don't know if the bug was solved, but you can use TCGAbiolinks(https://www.bioconductor.org/packages/devel/bioc/html/TCGAbiolinks.html) to download TCGA data and integrate with ELMER.

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