Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis21k
Reputation:
20,910
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Trusted
Location:
United States
Website:
http://watson.nci.nih....
Twitter:
@seandavis12
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Google Scholar Page
Last seen:
2 weeks, 5 days ago
Joined:
10 years ago
Email:
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Posts by Sean Davis

<prev • 2,133 results • page 2 of 214 • next >
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News: Invitation to submit articles to the Bioconductor gateway on F1000Research
... We invite you to contribute to a series of articles that will accompany the BioC 2018 conference in the Bioconductor gateway on F1000Research. We are specifically looking for: Cross-package workflows Package-based vignettes that show how to solve a scientific problem end-to-end Teachi ...
news publication written 12 weeks ago by Sean Davis21k
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Comment: C: processing deseq2 result
... Hello me37uday! It appears that your post has been cross-posted to another site: See https://www.biostars.org/p/304718/. This is typically not recommended as it runs the risk of annoying people in both communities. ...
written 3 months ago by Sean Davis21k
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Comment: C: Upregulation and Downregulation of Gene Ontology terms
... Could you clarify how this relates to Bioconductor by editing your question?  ...
written 3 months ago by Sean Davis21k
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Answer: C: getGEO error when trying to download a series matrix file
... It looks like you are using a pretty old version of R/Bioconductor. I suspect that an upgrade to R and then re-installing GEOquery will fix the problem.  ...
written 3 months ago by Sean Davis21k
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Comment: C: GEO2R Gene Expression
... tabler = function(g, gene_id) { vals = exprs(g)[gene_id, ] pd = pData(g) return(data.frame(sample = sampleNames(g), title=pd$title, values = vals )) } tabler(g, "assembledIsotigs_Contig9526") ...
written 3 months ago by Sean Davis21k
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Answer: A: GEO2R Gene Expression
... How about something like this: ​library(GEOquery) g = getGEO('GSE36545')[[1]] barplot(exprs(g)['assembledIsotigs_Contig9526', ], horiz = TRUE, las=2, cex.names = 0.5) Tinker with the plot to order samples as you see fit. For example, to order by tumor status: barplot(exprs(g)['assembledIsotigs_ ...
written 3 months ago by Sean Davis21k
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Answer: A: GEOquery: Diagnosing SOFT file error
... The error you are getting has to do with specifying GSEMatrix=F. If you use the default instead, you will get a list of ExpressionSets. Unfortunately, though, in this case, that will not help much to get access to the actual expression values. This GSE has only the metadata attached to the GSE file ...
written 3 months ago by Sean Davis21k
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Comment: C: getGEO Error: Duplicate identifiers for rows
... Should be fixed. ...
written 3 months ago by Sean Davis21k
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Answer: A: getGEO Error: Duplicate identifiers for rows
... This was a bug. It should be fixed in the next version in the Bioc-Devel (2.47.18) and in Bioc-Release (2.46.15). You can install from the GEOquery github repository if you need a quicker solution.  ...
written 3 months ago by Sean Davis21k
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Comment: C: getGEO Error: Duplicate identifiers for rows
... This is a bug due to a "feature" of this particular dataset in GEO (the same metadata key is used more than once per sample). I'll get a fix out in the next day or two.  ...
written 3 months ago by Sean Davis21k

Latest awards to Sean Davis

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: How to check the read length for all the TCGA data samples in GDC?
Appreciated 14 months ago, created a post with more than 5 votes. For Bioconductor packages now each have a DOI.
Appreciated 14 months ago, created a post with more than 5 votes. For Invitation to submit articles to the Bioconductor gateway on F1000Research
Appreciated 14 months ago, created a post with more than 5 votes. For Accessing Public Genomic Data from Bioconductor
Popular Question 14 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Guru 14 months ago, received more than 100 upvotes.
Scholar 14 months ago, created an answer that has been accepted. For A: SummarizedExperiment object from GEOquery obtained GSE
Scholar 14 months ago, created an answer that has been accepted. For A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
Scholar 14 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Scholar 14 months ago, created an answer that has been accepted. For A: getGEO Error: Duplicate identifiers for rows
Scholar 14 months ago, created an answer that has been accepted. For C: getGEO error when trying to download a series matrix file
Scholar 14 months ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: SummarizedExperiment object from GEOquery obtained GSE
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Adding a column to phenoData dataframe
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: GEOquery: 0 features in the gset object
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Scholar 2.2 years ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Popular Question 2.2 years ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Appreciated 2.2 years ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Scholar 2.4 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"

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