Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis20k
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20,430
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United States
Website:
http://watson.nci.nih....
Twitter:
@seandavis12
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Google Scholar Page
Last seen:
3 weeks, 4 days ago
Joined:
9 years, 3 months ago
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Posts by Sean Davis

<prev • 2,066 results • page 1 of 207 • next >
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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 25 days ago by Sean Davis20k
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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 4 weeks ago by Sean Davis20k
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Comment: C: Unused argument of reader = read_tsv on R version 3.4.1
... Did you re-install tximport after your R upgrade? If so, what is the output of `sessionInfo()`? If not, you should reinstall all your Bioconductor packages after the upgrade of R and then retry. ...
written 4 weeks ago by Sean Davis20k
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Comment: C: Bioconductor packages now each have a DOI.
... Yes, it resolves to https://bioconductor.org/packages/PACKAGENAME. Note the http(s), also. ...
written 4 weeks ago by Sean Davis20k
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News: Bioconductor packages now each have a DOI.
... DOIs are available for Bioconductor packages, one per package (no versions). All are of the form: doi:10.18129/B9.bioc.PACKAGENAME These DOIs resolve to the package landing page on Bioconductor. https://doi.org/10.18129/B9.bioc.Biobase The package names are case-insensitive. Feedback, ideas fo ...
news citation doi written 4 weeks ago by Sean Davis20k • updated 17 days ago by Martin Morgan ♦♦ 20k
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Answer: A: Retrieving data from NCBI GEO Problem and RNA-Seq Data Analysis
... Echoing the answer by Aaron, here is the code to download all supplemental files for a given GEO accession. library(GEOquery) sfiles = getGEOSuppFiles('GSE80336') fnames = rownames(sfiles) # there is only one supplemental file b2 = read.delim(fnames[1],header=TRUE) head(b2) ...
written 5 weeks ago by Sean Davis20k
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Answer: A: Problem with GEOquery R package in Windows when trying to download specific GEO
... The GEO Series Matrix files are a reflection of what is submitted.  Unfortunately, the submitters did not submit any normalized values.  Instead, they submitted only the .CEL files, it appears.  So, you are stuck with needing to download the .CEL files and processing those as raw data.  That isn't n ...
written 5 months ago by Sean Davis20k
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Comment: C: getGEO function not identifying local file
... Make sure that the file exists, that the download completed (the file size should be bigger than 0, at least), and that you are specifying the path to the file correctly. ...
written 6 months ago by Sean Davis20k
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Answer: A: Error in "getGSEDataTables" in GSEquery package
... Sorry I missed this question the first time.  The solution is to upgrade to GEOquery 2.40 or higher due to a change at NCBI from "http" to "https".  ...
written 9 months ago by Sean Davis20k
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Comment: C: CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
... Thanks, Val.  row.names=FALSE is a good solution for our use case. If unique IDs are of interest, hashing approaches would be potentially interesting to folks, but perhaps that is best left as a user-level decision. Part of my rationale for asking was to see what others thought.  ...
written 9 months ago by Sean Davis20k

Latest awards to Sean Davis

Teacher 6 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Scholar 17 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Appreciated 17 months ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question 17 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Popular Question 17 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 17 months ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 17 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 17 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: very high adjusted P-vals using Illumina data from GEO
Scholar 20 months ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Voter 20 months ago, voted more than 100 times.
Appreciated 23 months ago, created a post with more than 5 votes. For Bioc2015 conference ongoing now.
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: differential gene expression
Student 2.3 years ago, asked a question with at least 3 up-votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Scholar 2.6 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Scholar 2.6 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Supporter 2.7 years ago, voted at least 25 times.
Appreciated 2.8 years ago, created a post with more than 5 votes. For A: differential gene expression
Scholar 2.9 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Scholar 2.9 years ago, created an answer that has been accepted. For A: Processing RAW CEL files from GEO
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Oracle 3.0 years ago, created more than 1,000 posts (questions + answers + comments).
Centurion 3.0 years ago, created 100 posts.

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