Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis ♦ 21k
Reputation:
21,120
Status:
Trusted
Location:
United States
Website:
http://watson.nci.nih....
Twitter:
@seandavis12
Scholar ID:
Google Scholar Page
Last seen:
1 month, 1 week ago
Joined:
11 years ago
Email:
s*******@gmail.com

Posts by Sean Davis

<prev • 2,162 results • page 1 of 217 • next >
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Answer: A: TCGA MAF (Mutations) data
... MAF files contain only "positive" data. Lack of a mutation may mean that the patient did not have a mutation (true negative), was not tested for that mutation (panel did not cover the gene/location of interest), the mutation was "present" but filtered out in post-processing, or that the mutation was ...
written 5 weeks ago by Sean Davis ♦ 21k
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Comment: C: GEOquery: HTTP error 403
... The problem, at least for now, appears to be resolved. ...
written 7 weeks ago by Sean Davis ♦ 21k
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Comment: C: GEOquery: HTTP error 403
... Yes, to be clear, this is a problem at NCBI. There is nothing to be done with the GEOquery package to fix this. ...
written 7 weeks ago by Sean Davis ♦ 21k
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Comment: C: GEOquery: HTTP error 403
... This is a problem at NCBI. I've reported the issue and it will hopefully be resolved soon. ...
written 7 weeks ago by Sean Davis ♦ 21k
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Answer: A: GenomicDataCommons request timeouts when cases() %>% ... %>% results_all()
... 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 4 months ago by Sean Davis ♦ 21k
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Comment: C: edgeR. Known cancer genes are not differentially expressed?
... If you are looking for signals associated with groups of genes, perhaps you want to consider gene set enrichment analysis approaches. As for low logFC, those are not that unusual in human tumor systems. I cannot say with certainty that nothing you are doing is incorrect, but I would not necessarily ...
written 6 months ago by Sean Davis ♦ 21k
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Comment: C: geGeo error - Error in .subset2(x, i) : subscript out of bounds
... Thanks for the report. Others have noticed this problem, again apparently related to recent changes in readr. You can follow progress here: https://github.com/seandavi/GEOquery/issues/78 ...
written 6 months ago by Sean Davis ♦ 21k
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Comment: C: GEOquery:Get error sampleNames
... Just a quick update--the Rstudio team has a working fix and it is going through code review. Once that is completed and the new readr package is released, the GEOquery problem will be resolved.  ...
written 6 months ago by Sean Davis ♦ 21k
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Comment: C: GEOQuery bug, NCBI or package?
... Just a quick update--the Rstudio team has a working fix and it is going through code review. Once that is completed and the new readr package is released, the GEOquery problem will be resolved.  ...
written 6 months ago by Sean Davis ♦ 21k
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Comment: C: GEOQuery bug, NCBI or package?
... This is a bug due to a change in behavior of the readr read_tsv function. https://github.com/tidyverse/readr/issues/925. There is an ongoing conversation about what to do here. Sorry for the instability. ...
written 6 months ago by Sean Davis ♦ 21k

Latest awards to Sean Davis

Popular Question 7 months ago, created a question with more than 1,000 views. For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Popular Question 9 months ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Scholar 9 months ago, created an answer that has been accepted. For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
Scholar 11 months ago, created an answer that has been accepted. For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
Scholar 11 months ago, created an answer that has been accepted. For A: Using eset while parsing GSE file located in a path
Popular Question 13 months ago, created a question with more than 1,000 views. For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Scholar 2.2 years ago, created an answer that has been accepted. For A: SummarizedExperiment object from GEOquery obtained GSE
Scholar 2.2 years ago, created an answer that has been accepted. For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
Scholar 2.2 years ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Scholar 2.2 years ago, created an answer that has been accepted. For A: getGEO Error: Duplicate identifiers for rows
Scholar 2.2 years ago, created an answer that has been accepted. For C: getGEO error when trying to download a series matrix file
Scholar 2.2 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: SummarizedExperiment object from GEOquery obtained GSE
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Adding a column to phenoData dataframe
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: How to check the read length for all the TCGA data samples in GDC?
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: GEOquery: 0 features in the gset object
Appreciated 2.2 years ago, created a post with more than 5 votes. For Bioconductor packages now each have a DOI.
Appreciated 2.2 years ago, created a post with more than 5 votes. For Invitation to submit articles to the Bioconductor gateway on F1000Research
Appreciated 2.2 years ago, created a post with more than 5 votes. For Accessing Public Genomic Data from Bioconductor
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Guru 2.2 years ago, received more than 100 upvotes.
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Popular Question 3.2 years ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Appreciated 3.2 years ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
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