Moderator: Sean Davis

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Sean Davis21k
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http://watson.nci.nih....
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@seandavis12
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Posts by Sean Davis

<prev • 2,166 results • page 1 of 217 • next >
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Answer: A: Annotation Using GEOquery
... As for the annotation from GEOquery, the `fData` accessor will access the feature data that the submitter supplied to GEO. ``` g = getGEO("GSE51469")[[1]] head(fData(g)) ``` In your case, it appears that the only informative column is the "SEQUENCE" column which you could use to BLAST against gene ...
written 4 weeks ago by Sean Davis21k
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Comment: C: Annotation Using GEOquery
... The problems you are having above are not related to Bioconductor. You might want to spend a little time taking a quick intro-to-R course. ...
written 4 weeks ago by Sean Davis21k
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Comment: C: GEOquery and Feature data
... In your `select` above, you'll need to use an Annotation database, not GEOquery. You also seem to have a fair number of typos, so you may benefit from a little instruction in using R, as having a foundation in the basics or R is valuable for using Bioconductor. ...
written 4 weeks ago by Sean Davis21k
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Answer: A: Downloading a private GEO with GEOquery
... 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 weeks ago by Sean Davis21k
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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 7 months ago by Sean Davis21k
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Comment: C: GEOquery: HTTP error 403
... The problem, at least for now, appears to be resolved. ...
written 7 months ago by Sean Davis21k
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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 months ago by Sean Davis21k
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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 months ago by Sean Davis21k
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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 10 months ago by Sean Davis21k
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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 12 months ago by Sean Davis21k

Latest awards to Sean Davis

Appreciated 11 months ago, created a post with more than 5 votes. 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 Invitation to submit articles to the Bioconductor gateway on F1000Research
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 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 15 months ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Scholar 17 months ago, created an answer that has been accepted. For A: Using eset while parsing GSE file located in a path
Scholar 17 months ago, created an answer that has been accepted. For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
Popular Question 19 months ago, created a question with more than 1,000 views. For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
Scholar 2.7 years ago, created an answer that has been accepted. For C: getGEO error when trying to download a series matrix file
Teacher 2.7 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 2.7 years ago, created an answer with at least 3 up-votes. For A: GEOquery: 0 features in the gset object
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: Adding a column to phenoData dataframe
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: SummarizedExperiment object from GEOquery obtained GSE
Scholar 2.7 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Scholar 2.7 years ago, created an answer that has been accepted. For A: getGEO Error: Duplicate identifiers for rows
Scholar 2.7 years ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Scholar 2.7 years ago, created an answer that has been accepted. For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
Scholar 2.7 years ago, created an answer that has been accepted. For A: SummarizedExperiment object from GEOquery obtained GSE
Guru 2.7 years ago, received more than 100 upvotes.
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Appreciated 2.7 years ago, created a post with more than 5 votes. For Accessing Public Genomic Data from Bioconductor
Appreciated 2.7 years ago, created a post with more than 5 votes. For Invitation to submit articles to the Bioconductor gateway on F1000Research
Appreciated 2.7 years ago, created a post with more than 5 votes. For Bioconductor packages now each have a DOI.
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File

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