Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis21k
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United States
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http://watson.nci.nih....
Twitter:
@seandavis12
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Joined:
9 years, 5 months ago
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Posts by Sean Davis

<prev • 2,084 results • page 2 of 209 • next >
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Answer: A: How to construct an up-to-date and annotation-rich RangeSummarizedExperiment obj
... Unfortunately, there is not a single, simple approach here and the outline I give is without any testing. That said, you could use the UNIGENE ids to map back to ENTREZGENE id's using the org.hs.eg.db package. From the ENTREZ IDs, you can map to transcripts via the appropriate transcriptdb object. T ...
written 17 days ago by Sean Davis21k
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Comment: C: Comparing one condition to multiple others using DESeq2 contrasts
... Take a look at using `combn()` and a loop.  ...
written 22 days ago by Sean Davis21k
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Answer: A: Comparing one condition to multiple others using DESeq2 contrasts
... Contrasts are usually between two specific groups. In your case, it appears that you want to compare `S1` to each of `S2` through `S4`. That is most easily accomplished by three separate calls to `results()`. Using a loop over a set of groups is also a possibility for a larger number of groups but m ...
written 23 days ago by Sean Davis21k
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Answer: A: Subsetting samples and columns of a MethyLumiSet subsets QC probes
... Thanks for the report. This should be fixed in 2.24.1 (release) and 2.25.1 (devel) versions. ...
written 24 days ago by Sean Davis21k
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Comment: C: problem with getSRAfile in SRAdb
... SRAdb just downloads the file from the link in your post, so this isn't really a problem with SRAdb specifically, I suspect. Could you try doing the download outside of R? Also, could you check the file size on your disk as well as the value reported by R? ...
written 25 days ago by Sean Davis21k
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Answer: A: Changing R package dependencies
... You would need to: Download the source package. Modify the DESCRIPTION file (at least) Install from source. Doing so is very likely to lead to a broken package, so I do not recommend doing so. In your case, it appears that you want to use mm10 instead of mm9. I would suggest installing the pa ...
written 4 weeks ago by Sean Davis21k
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Comment: C: DOI for packages
... Good point, Henrik. The DOI actually resolves to https://bioconductor.org/packages/PKGNAME, by design. Then, things are redirected as needed from that URL to either release or devel. We will need to develop a standard landing page for packages that have been removed contains useful information to th ...
written 5 weeks ago by Sean Davis21k
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Comment: C: Trouble with multtest
... You showed us the error, but not the code that produced it. Could you show the rest of the code? ...
written 5 weeks ago by Sean Davis21k
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Comment: C: GEOquery download error
... There are sometimes intermittent connection problems to GEO. Could you try again a few hours after your last try? ...
written 12 weeks ago by Sean Davis21k
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Comment: C: Bioconductor packages now each have a DOI.
... Yes, the process is currently kicked off manually. In addition, new DOIs and changes to existing ones can take some time to propagate to resolvers.  ...
written 3 months ago by Sean Davis21k

Latest awards to Sean Davis

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Scholar 19 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Appreciated 19 months ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question 19 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Popular Question 19 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 19 months ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 19 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 19 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: very high adjusted P-vals using Illumina data from GEO
Scholar 22 months ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Voter 22 months ago, voted more than 100 times.
Appreciated 2.1 years ago, created a post with more than 5 votes. For Bioc2015 conference ongoing now.
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: differential gene expression
Student 2.5 years ago, asked a question with at least 3 up-votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Scholar 2.8 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Scholar 2.8 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Supporter 2.8 years ago, voted at least 25 times.
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: differential gene expression
Scholar 3.0 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Scholar 3.1 years ago, created an answer that has been accepted. For A: Processing RAW CEL files from GEO
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