Moderator: Sean Davis
Sean Davis ♦ 25k
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- National Institutes of Health, Bethesda, MD
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- http://watson.nci.nih....
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Posts by Sean Davis
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... I should clean up the documentation, but `results_all()` is a convenience wrapper that is not too smart in that it simply tries to return all results in one trip to the server. This can fail for multiple reasons related to the size of result sets. The better approach (and the only one in the case of ...
written 8 weeks ago by
Sean Davis ♦ 25k
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... See: https://support.bioconductor.org/p/114340/#114357 for the answer. ...
written 4 months ago by
Sean Davis ♦ 25k
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... GEOmetadb contains only the "metadata", not the actual RNA-seq counts. You can use GEOquery to access the actual data, if they have been submitted, or you can download fastq from SRA if you have access to the studies (since it appears you are working in human, these files will be protected). ...
written 7 months ago by
Sean Davis ♦ 25k
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... The ICGC is not the right place to get access to TCGA controlled-access data, as you point out. To gain access to controlled-access TCGA data, one needs to apply through dbGaP. The process is documented here:
https://gdc.cancer.gov/access-data/obtaining-access-controlled-data
After approval for co ...
written 11 months ago by
Sean Davis ♦ 25k
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... We invite you to contribute to a series of articles that will accompany the BioC 2018 conference in the [Bioconductor gateway on F1000Research][1]. We are specifically looking for:
- Cross-package workflows
- Package-based vignettes that show how to solve a scientific problem end-to-end
- Teaching ...
written 11 months ago by
Sean Davis ♦ 25k
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... Using a GSEA approach where one study's DEG list is the "gene set" which you can test for enrichment in the other will give you a statistical result. I think this is one answer for both of your questions.
There are other ways to look at individual gene-level results, including meta-analysis. ...
written 11 months ago by
Sean Davis ♦ 25k
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... What data are you trying to get? Gene expression, clinical? ...
written 11 months ago by
Sean Davis ♦ 25k
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654
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... GSE18 has nine different platforms (microarray types). The GDS records each represent one of those microarray types. ...
written 11 months ago by
Sean Davis ♦ 25k
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... Some submissions have undergone a curation process at GEO, giving them a GDS accession. NCBI has not been curating data for several years, so the GDS accessions are historical and now represent a pretty small proportion of the GEO information. A GDS and GSE represent pretty much the same type of dat ...
written 11 months ago by
Sean Davis ♦ 25k
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... [netsig](https://www.nature.com/articles/nmeth.4514) is a new one. ...
written 11 months ago by
Sean Davis ♦ 25k
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