Moderator: Sean Davis

gravatar for Sean Davis
Sean Davis21k
Reputation:
20,690
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Location:
United States
Website:
http://watson.nci.nih....
Twitter:
@seandavis12
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Google Scholar Page
Last seen:
1 week, 1 day ago
Joined:
9 years, 8 months ago
Email:
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Posts by Sean Davis

<prev • 2,113 results • page 1 of 212 • next >
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Comment: C: Performing differential gene analysis on RT PCR experimental data
... The values are reported by the submitter to be "batch-corrected deltaCT" values. ...
written 16 days ago by Sean Davis21k
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Comment: C: How to identify Disease biomarkers " DNA sequences as biomarkers "
... https://biomarkerres.biomedcentral.com/articles ...
written 16 days ago by Sean Davis21k
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Answer: A: Are two biological replicates enough for a transcriptome analysis using DESeq2?
... Two replicates is fine, operationally. Whether or not two replicates is "enough" for your experiment is something that is hard to comment on without more information. As an aside, I would note that using PCA to remove "outliers" when there are only three samples per group runs the risk of removing ...
written 23 days ago by Sean Davis21k
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Comment: C: DEGs of microarray Data and hierarchical clustering and visualizing using heatma
... Having code is really one of the best ways to get a clear answer. To get your heatmap, you might want to try using `exprs(my_expressionset)` rather than `exprs(fit2)` ...
written 23 days ago by Sean Davis21k
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Comment: C: DEGs of microarray Data and hierarchical clustering and visualizing using heatma
... Have you read the limma user guide? If so, post the code you have tried. If not, that is the place to start. ...
written 23 days ago by Sean Davis21k
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Comment: C: ExpressionSet annotation with custom annotation file
... To remove rows from anno that do not map to an "ENSG", you can do something like: anno_no_ensg = anno[!grepl('ENSG';, anno$ENSEMBL),] I suspect that is only half of the problem. You will likely still have the problem of a single probe_id mapping to multiple ENSGs. Unfortunately, that is not a simple ...
written 23 days ago by Sean Davis21k
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Comment: C: SRAdb: Error downloading sqlite files
... Newer versions of SRAdb have fixed this issue. Upgrading should allow the `getSRAdbFile()` function to work again.  ...
written 27 days ago by Sean Davis21k
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Comment: C: GEOquery http:// url error
... NCBI GEO does know about the old version of R and Bioconductor; hopefully they will be able to upgrade soon.  ...
written 29 days ago by Sean Davis21k
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Comment: C: GEOquery http:// url error
... You could consider using the Bioconductor AMI to run Bioconductor in the cloud which would allow you the option of using an R version you do not have locally. The analysis you are doing should cost just $0.10 or so. http://bioconductor.org/help/bioconductor-cloud-ami/ ...
written 29 days ago by Sean Davis21k
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Answer: A: GEOquery http:// url error
... Please upgrade to the newest R version (currently 3.4.x series) and then reinstall Bioconductor/GEOquery (see here: https://www.bioconductor.org/install/). That should fix this issue.  ...
written 29 days ago by Sean Davis21k

Latest awards to Sean Davis

Teacher 11 months ago, created an answer with at least 3 up-votes. For A: GEOquery Fails to Download Series Matrix File
Scholar 22 months ago, created an answer that has been accepted. For A: GEOquery Fails to Download Series Matrix File
Appreciated 22 months ago, created a post with more than 5 votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Popular Question 22 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Popular Question 22 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 22 months ago, created a question with more than 1,000 views. For dplyr and the GEOmetadb package for mining NCBI GEO metadata
Popular Question 22 months ago, created a question with more than 1,000 views. For Accessing Public Genomic Data from Bioconductor
Popular Question 22 months ago, created a question with more than 1,000 views. For Illumina Expression analysis from iDAT files
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: very high adjusted P-vals using Illumina data from GEO
Scholar 2.1 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Voter 2.1 years ago, voted more than 100 times.
Appreciated 2.3 years ago, created a post with more than 5 votes. For Bioc2015 conference ongoing now.
Appreciated 2.6 years ago, created a post with more than 5 votes. For A: differential gene expression
Student 2.7 years ago, asked a question with at least 3 up-votes. For Bootstrap confidence intervals on RNA-seq expression from Kallisto
Scholar 3.0 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Scholar 3.0 years ago, created an answer that has been accepted. For A: Transitive overlaps of GRanges object
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Supporter 3.1 years ago, voted at least 25 times.
Appreciated 3.2 years ago, created a post with more than 5 votes. For A: differential gene expression
Scholar 3.3 years ago, created an answer that has been accepted. For A: SRAdb: could not find function "sqliteTableFields"
Scholar 3.3 years ago, created an answer that has been accepted. For A: Processing RAW CEL files from GEO
Teacher 3.4 years ago, created an answer with at least 3 up-votes. For A: differential gene expression
Oracle 3.5 years ago, created more than 1,000 posts (questions + answers + comments).
Centurion 3.5 years ago, created 100 posts.

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