Moderator: Sean Davis
Sean Davis ♦ 21k
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Posts by Sean Davis
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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 Davis ♦ 21k
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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 Davis ♦ 21k
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57
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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 Davis ♦ 21k
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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 weeks ago by
Sean Davis ♦ 21k
1
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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 Davis ♦ 21k
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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 Davis ♦ 21k
1
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1
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401
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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 Davis ♦ 21k
0
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1
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401
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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 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 10 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 12 months ago by
Sean Davis ♦ 21k
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11 months ago,
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For Invitation to submit articles to the Bioconductor gateway on F1000Research
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11 months ago,
created a question with more than 1,000 views.
For Invitation to submit articles to the Bioconductor gateway on F1000Research
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For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
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For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
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For dplyr and the GEOmetadb package for mining NCBI GEO metadata
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For A: Using eset while parsing GSE file located in a path
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For A: Filtering Gene Symbols and Sample Description from GSE files of GEO
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For Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
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For C: getGEO error when trying to download a series matrix file
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For A: How to check the read length for all the TCGA data samples in GDC?
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For A: GEOquery: 0 features in the gset object
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For A: GEOquery Fails to Download Series Matrix File
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For A: Adding a column to phenoData dataframe
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For A: SummarizedExperiment object from GEOquery obtained GSE
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For A: SRAdb: could not find function "sqliteTableFields"
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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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For A: GEOquery Fails to Download Series Matrix File
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