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Invalid gene in mutation-matrix.tsv.bz2 on figshare v5 #36

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dhimmel opened this issue Dec 9, 2016 · 1 comment
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Invalid gene in mutation-matrix.tsv.bz2 on figshare v5 #36

dhimmel opened this issue Dec 9, 2016 · 1 comment

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@dhimmel
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dhimmel commented Dec 9, 2016

See cognoma/core-service#42 (comment), where @stephenshank has discovered a gene with an invalid entrez_gene_id in mutation-matrix.tsv.bz2 from https://doi.org/10.6084/m9.figshare.3487685.v5.

The gene is 117153, which is not included in genes.tsv.

@dhimmel
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dhimmel commented Jan 4, 2017

@stephenshank I figured out the issue 🤞:

  • Version 5 on figshare was based on b054721, which predates the cognoma/genes integration.

  • Version 6 on figshare, which I just uploaded, is based on the current repository (1d961fb).

So hopefully if you update to version 6 the issues will be fixed. Sorry about that -- my bad with not updating the figshare.

@vasudevanv, this is the sort of mistake that continuous deposition would solve -- basically any time the cancer-data code is updated the datasets are regenerated and uploaded to figshare. Not that this is worth the time to implement, but it's the way of the future.

@dhimmel dhimmel closed this as completed Jan 4, 2017
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