Moderator: Sean Davis

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Sean Davis20k
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http://watson.nci.nih....
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Posts by Sean Davis

<prev • 2,060 results • page 1 of 206 • next >
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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 3 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 4 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 7 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 7 months ago by Sean Davis20k
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CollapsedVCF and ExpandedVCF rownames and vcfs with large ref/alt columns
... 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 ...
variantannotation vcf written 7 months ago by Sean Davis20k • updated 7 months ago by Valerie Obenchain ♦♦ 6.2k
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Comment: C: Reading files from Softlayer Object Storage
... https://github.com/IBMDataScience/objectStoreR/issues/2 ...
written 8 months ago by Sean Davis20k
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Answer: A: Reading files from Softlayer Object Storage
... 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 Davis20k
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Comment: C: How to start CrispRVariants with fastq file starting point
... 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. ...
written 8 months ago by Sean Davis20k
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Problem with VariantAnnotation and VCF "R" genotype fields when expanding CollapsedVCF
... 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 ...
variantannotation bug written 8 months ago by Sean Davis20k • updated 7 months ago by Valerie Obenchain ♦♦ 6.2k
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Answer: A: GEOquery error in downloading SOFT files
... 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 Davis20k

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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