Moderator: Sean Davis

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Sean Davis21k
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United States
Website:
http://watson.nci.nih....
Twitter:
@seandavis12
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Last seen:
19 hours ago
Joined:
9 years, 5 months ago
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Posts by Sean Davis

<prev • 2,081 results • page 1 of 209 • next >
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Comment: C: Using limma analyze raw data of illumina beadchip
... What is the analysis you want to do? ...
written 2 days ago by Sean Davis21k
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Comment: C: for loop not working!
... This site is for support for Bioconductor, not for general R questions. I'd suggest trying stackoverflow if you still have problems after reading more about loops in R.  ...
written 2 days ago by Sean Davis21k
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Comment: C: DESeq2 biais when genes are missing from the annotation?
... And how about at the genomic level?  ...
written 7 days ago by Sean Davis21k
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Comment: C: DESeq2 biais when genes are missing from the annotation?
... Do you expect or observe that the proportion of unmapped reads is different across groups or samples?  ...
written 8 days ago by Sean Davis21k
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Answer: A: how to obtain differentially expressed genes from a GSE serie
... Use GSEMatrix = TRUE. The result from getGEO is a list, so use only the first element. GSE16444 <- getGEO('GSE16444', GSEMatrix = TRUE) The GSE16444 is now an ExpressionSet that can be used in any package that performs differential expression analysis starting from there. Limma is an appropriat ...
written 8 days ago by Sean Davis21k
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Answer: A: Cannot download GEOmetadb sqlite file
... Sorry for the recent instability. We have switched the GEOmetadb package over to AWS hosting as we did with SRAdb. I just made the change to GEOmetadb in both release and devel, so expect the change to be available from bioconductor in about 36 hours or so. If you need something sooner, installing f ...
written 12 days ago by Sean Davis21k
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Comment: C: How to construct an up-to-date and annotation-rich RangeSummarizedExperiment obj
... I'd say give it a try. ...
written 13 days ago by Sean Davis21k
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Answer: A: How to construct an up-to-date and annotation-rich RangeSummarizedExperiment obj
... Unfortunately, there is not a single, simple approach here and the outline I give is without any testing. That said, you could use the UNIGENE ids to map back to ENTREZGENE id's using the org.hs.eg.db package. From the ENTREZ IDs, you can map to transcripts via the appropriate transcriptdb object. T ...
written 13 days ago by Sean Davis21k
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Comment: C: Comparing one condition to multiple others using DESeq2 contrasts
... Take a look at using `combn()` and a loop.  ...
written 19 days ago by Sean Davis21k
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Answer: A: Comparing one condition to multiple others using DESeq2 contrasts
... Contrasts are usually between two specific groups. In your case, it appears that you want to compare `S1` to each of `S2` through `S4`. That is most easily accomplished by three separate calls to `results()`. Using a loop over a set of groups is also a possibility for a larger number of groups but m ...
written 20 days ago by Sean Davis21k

Latest awards to Sean Davis

Teacher 8 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Scholar 19 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Appreciated 19 months ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question 19 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Popular Question 19 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 19 months ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 19 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 19 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: very high adjusted P-vals using Illumina data from GEO
Scholar 22 months ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Voter 22 months ago, voted more than 100 times.
Appreciated 2.1 years ago, created a post with more than 5 votes. For Bioc2015 conference ongoing now.
Appreciated 2.3 years ago, created a post with more than 5 votes. For A: differential gene expression
Student 2.5 years ago, asked a question with at least 3 up-votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Scholar 2.8 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Scholar 2.8 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Teacher 2.8 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Supporter 2.8 years ago, voted at least 25 times.
Appreciated 3.0 years ago, created a post with more than 5 votes. For A: differential gene expression
Scholar 3.0 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Scholar 3.1 years ago, created an answer that has been accepted. For A: Processing RAW CEL files from GEO
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Oracle 3.2 years ago, created more than 1,000 posts (questions + answers + comments).
Centurion 3.2 years ago, created 100 posts.

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