Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis21k
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United States
Website:
http://watson.nci.nih....
Twitter:
@seandavis12
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5 days, 13 hours ago
Joined:
9 years, 8 months ago
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Posts by Sean Davis

<prev • 2,113 results • page 2 of 212 • next >
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Answer: A: GEOquery getGEO 404
... Please upgrade to the most recent R (at least version 3.4) and Bioconductor (https://www.bioconductor.org/install/). This error has been addressed in more recent versions of GEOquery. ...
written 26 days ago by Sean Davis21k
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Comment: C: Patch for GEOquery package error: getGEO Error in download.file, cannot open des
... Thanks for the kind words. If, after you have updated to R-3.4.3, you still see the error, definitely file an issue. I suspect that upgrading R and then re-installing the current release version of GEOquery will fix the issue. In general, we do not fix outdated versions of Bioconductor but, instead, ...
written 26 days ago by Sean Davis21k
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Comment: C: Patch for GEOquery package error: getGEO Error in download.file, cannot open des
... While it can be tempting to suggest to the community that cutting-and-pasting a "patch" into a seemingly problematic package, please refrain from doing so, as it negates the benefits of version control including reproducibility in the software workflow and sidesteps the Bioconductor testing and chec ...
written 26 days ago by Sean Davis21k
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Comment: C: Patch for GEOquery package error: getGEO Error in download.file, cannot open des
... Can you post the output of `sessionInfo()`? I suspect you are using an outdated version of GEOquery.  ...
written 26 days ago by Sean Davis21k
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Comment: C: Problem in installing Bioconductor packages due to "IRanges"
... What is the output of `sessionInfo()` after you load IRanges?  ...
written 6 weeks ago by Sean Davis21k
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Answer: A: How to check if the microarray data is from codelink
... The official (supplied by codelink) GEO Platform (GPL) is: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL2895 The GPL record contains information about associated samples and series. The following will provide the series IDs associated with the codelink platform: gpl = getGEO("GPL2895") Meta ...
written 6 weeks ago by Sean Davis21k
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Comment: C: SummarizedExperiment object from GEOquery obtained GSE
... The regex is matched directly against filenames, not file contents. The default behavior when no regex is specified is to fetch all supplemental files, so the .tar file will be downloaded by default.  ...
written 6 weeks ago by Sean Davis21k
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Comment: C: SummarizedExperiment object from GEOquery obtained GSE
... Great. Let me know if you have any problems or have further suggestions on the GEOquery side of things.  ...
written 6 weeks ago by Sean Davis21k
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Answer: A: SummarizedExperiment object from GEOquery obtained GSE
... I have just updated the GEOquery getGEOSuppFiles() function (version 2.47.16) to support filtering supplemental files (filter_regex='bed') and to return a listing of files without download (fetch_files=FALSE). To give it a try immediately, install from github: biocLite('seandavi/GEOquery') In 24 ...
written 6 weeks ago by Sean Davis21k
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Comment: C: SummarizedExperiment object from GEOquery obtained GSE
... With 10 bed files, what would you want the ranges and the "assay" in the summarized experiment to contain? ...
written 6 weeks ago by Sean Davis21k

Latest awards to Sean Davis

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Scholar 22 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Appreciated 22 months ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question 22 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Popular Question 22 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 22 months ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 22 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 22 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: very high adjusted P-vals using Illumina data from GEO
Scholar 2.1 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Voter 2.1 years ago, voted more than 100 times.
Appreciated 2.3 years ago, created a post with more than 5 votes. For Bioc2015 conference ongoing now.
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: differential gene expression
Student 2.7 years ago, asked a question with at least 3 up-votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Scholar 3.0 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Scholar 3.0 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Supporter 3.1 years ago, voted at least 25 times.
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: differential gene expression
Scholar 3.3 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Scholar 3.3 years ago, created an answer that has been accepted. For A: Processing RAW CEL files from GEO
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Oracle 3.4 years ago, created more than 1,000 posts (questions + answers + comments).
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