Moderator: Sean Davis
Sean Davis ♦ 20k
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- Joined:
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Posts by Sean Davis
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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 Davis ♦ 20k
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... 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.
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written 4 weeks ago by
Sean Davis ♦ 20k
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... 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.
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written 4 weeks ago by
Sean Davis ♦ 20k
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... Yes, it resolves to https://bioconductor.org/packages/PACKAGENAME. Note the http(s), also.
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written 4 weeks ago by
Sean Davis ♦ 20k
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... 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 ...
written 4 weeks ago by
Sean Davis ♦ 20k
• updated 17 days ago by
Martin Morgan ♦♦ 20k
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... 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 Davis ♦ 20k
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... 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 Davis ♦ 20k
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701
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... 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.
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written 6 months ago by
Sean Davis ♦ 20k
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... 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".
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written 9 months ago by
Sean Davis ♦ 20k
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... 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 Davis ♦ 20k
Latest awards to Sean Davis
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6 months ago,
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For A: GEOquery Fails to Download Series Matrix File
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17 months ago,
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For A: GEOquery Fails to Download Series Matrix File
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17 months ago,
created a post with more than 5 votes.
For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question
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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
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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
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20 months ago,
created an answer that has been accepted.
For A: SRAdb: could not find function "sqliteTableFields"
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For Bioc2015 conference ongoing now.
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2.2 years ago,
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For A: differential gene expression
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2.3 years ago,
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For Bootstrap confidence intervals on RNA-seq expression from Kallisto
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2.6 years ago,
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For A: Transitive overlaps of GRanges object
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For A: differential gene expression
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For A: differential gene expression
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2.9 years ago,
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For A: SRAdb: could not find function "sqliteTableFields"
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2.9 years ago,
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For A: Processing RAW CEL files from GEO
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For A: differential gene expression
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