Moderator: Sean Davis
Sean Davis ♦ 20k
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- Website:
- http://watson.nci.nih....
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- Last seen:
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- Joined:
- 9 years, 1 month ago
- Email:
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Posts by Sean Davis
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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 3 months ago by
Sean Davis ♦ 20k
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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 4 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 7 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.
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written 7 months ago by
Sean Davis ♦ 20k
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... With some newer VCF files, particularly those that have come from structural variant callers, the rownames of the resulting `VCF` objects (when the ID column is missing) can become problematic or excessively large. To give a concrete example, we have VCFs with insertions of dozens or hundreds of bas ...
written 7 months ago by
Sean Davis ♦ 20k
• updated 7 months ago by
Valerie Obenchain ♦♦ 6.2k
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... https://github.com/IBMDataScience/objectStoreR/issues/2
...
written 8 months ago by
Sean Davis ♦ 20k
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... The objectStoreR package is VERY specific in that it only deals with CSV files. As a simple starting place, you could contact the author and ask if he/she is willing to write a objectstore.fetchToDisk() function that simply grabs an object and writes it to disk. That would allow you to interface wi ...
written 8 months ago by
Sean Davis ♦ 20k
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... Is there a reason that you cannot start at section 2.2 of that user guide? I believe that section assumes that you have fastq files already.
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written 8 months ago by
Sean Davis ♦ 20k
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... I noticed a numeric difference between the AD geno field when going from a CollapsedVCF to ExpandedVCF. Here is an example. I can share the VCF offline, as it is human data. In the example, it seems that after expansion, the AD numbers appear to not match the CollapsedVCF version.
> vcfCom ...
written 8 months ago by
Sean Davis ♦ 20k
• updated 7 months ago by
Valerie Obenchain ♦♦ 6.2k
0
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... An upgrade to GEOquery 2.40 will likely fix the problem. NCBI has moved away from using "http" in favor of "https", so you'll need to update GEOquery to address that issue. Sorry for the inconvenience!
...
written 8 months ago by
Sean Davis ♦ 20k
Latest awards to Sean Davis
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: GEOquery Fails to Download Series Matrix File
Scholar
15 months ago,
created an answer that has been accepted.
For A: GEOquery Fails to Download Series Matrix File
Appreciated
15 months ago,
created a post with more than 5 votes.
For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
Popular Question
15 months ago,
created a question with more than 1,000 views.
For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Accessing Public Genomic Data from Bioconductor
Popular Question
15 months ago,
created a question with more than 1,000 views.
For Illumina Expression analysis from iDAT files
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: very high adjusted P-vals using Illumina data from GEO
Scholar
18 months ago,
created an answer that has been accepted.
For A: SRAdb: could not find function "sqliteTableFields"
Voter
18 months ago,
voted more than 100 times.
Appreciated
21 months ago,
created a post with more than 5 votes.
For Bioc2015 conference ongoing now.
Appreciated
2.0 years ago,
created a post with more than 5 votes.
For A: differential gene expression
Student
2.1 years ago,
asked a question with at least 3 up-votes.
For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: Transitive overlaps of GRanges object
Scholar
2.4 years ago,
created an answer that has been accepted.
For A: Transitive overlaps of GRanges object
Teacher
2.4 years ago,
created an answer with at least 3 up-votes.
For A: differential gene expression
Supporter
2.5 years ago,
voted at least 25 times.
Appreciated
2.7 years ago,
created a post with more than 5 votes.
For A: differential gene expression
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: SRAdb: could not find function "sqliteTableFields"
Scholar
2.7 years ago,
created an answer that has been accepted.
For A: Processing RAW CEL files from GEO
Teacher
2.8 years ago,
created an answer with at least 3 up-votes.
For A: differential gene expression
Oracle
2.9 years ago,
created more than 1,000 posts (questions + answers + comments).
Centurion
2.9 years ago,
created 100 posts.
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