Moderator: Sean Davis
Sean Davis ♦ 21k
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Posts by Sean Davis
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... Unfortunately, I don't have that functionality implemented. You can download the series matrix files by hand and then read them using `getGEO`, though.
I will not be able to get to it soon, but if you want, feel free to file an issue to add reviewer link functionality (https://www.ncbi.nlm.nih.gov ...
written 9 days ago by
Sean Davis ♦ 21k
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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 months 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 5 months 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 5 months 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 5 months ago by
Sean Davis ♦ 21k
2
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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 months ago by
Sean Davis ♦ 21k
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... 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 10 months ago by
Sean Davis ♦ 21k
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... 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 10 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 10 months ago by
Sean Davis ♦ 21k
0
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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 10 months ago by
Sean Davis ♦ 21k
Latest awards to Sean Davis
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9 months ago,
created a post with more than 5 votes.
For Invitation to submit articles to the Bioconductor gateway on F1000Research
Popular Question
9 months ago,
created a question with more than 1,000 views.
For Invitation to submit articles to the Bioconductor gateway on F1000Research
Popular Question
11 months ago,
created a question with more than 1,000 views.
For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Scholar
13 months ago,
created an answer that has been accepted.
For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
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13 months ago,
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For dplyr and the GEOmetadb package for mining NCBI GEO metadata
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15 months ago,
created an answer that has been accepted.
For A: Using eset while parsing GSE file located in a path
Scholar
15 months ago,
created an answer that has been accepted.
For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Scholar
2.5 years ago,
created an answer that has been accepted.
For C: getGEO error when trying to download a series matrix file
Teacher
2.5 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
2.5 years ago,
created an answer with at least 3 up-votes.
For A: GEOquery: 0 features in the gset object
Teacher
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created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
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2.5 years ago,
created an answer with at least 3 up-votes.
For A: Adding a column to phenoData dataframe
Teacher
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For A: SummarizedExperiment object from GEOquery obtained GSE
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2.5 years ago,
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For A: SRAdb: could not find function "sqliteTableFields"
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2.5 years ago,
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For A: getGEO Error: Duplicate identifiers for rows
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For A: GEOquery Fails to Download Series Matrix File
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For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
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For A: SummarizedExperiment object from GEOquery obtained GSE
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For Illumina Expression analysis from iDAT files
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For Bioconductor packages now each have a DOI.
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2.6 years ago,
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For A: GEOquery Fails to Download Series Matrix File
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