Moderator: James W. MacDonald

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14 years, 10 months ago
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j******@u.washington.edu

I am a core member of the Bioconductor project, and I work for the University of Washington in the Department of Environmental and Occupational Health Sciences. I telecommute from Ann Arbor, MI (Go Blue!) because how will I be able to suffer the enduring pain of being a UM football fan if I can't go to the games?

Posts by James W. MacDonald

<prev • 4,755 results • page 2 of 476 • next >
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Answer: A: Regressing effect of treatment on RNA-seq expected count from rsem.
... You will want to first convert those data to something more amenable (than counts) for clustering. Alternatives include voom or cpm in edgeR, or rlog or vst in DESeq2. I won't go into arguments for or against any of those choices other than to say that they exist. Once you have converted using the ...
written 4 days ago by James W. MacDonald43k
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Answer: A: Error running the function permTest
... Part of permTest is to determine what the alternative hypothesis is, and if you don't specify the alternative, it will figure it out by itself (which is sort of bootleg - you shouldn't decide on the test based on your data, but whatever). It does this by looking at the mean of the randomized data (w ...
written 4 days ago by James W. MacDonald43k
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Answer: A: Running DESeq2 inside local Galaxy instance
... This doesn't really seem like a Bioconductor question. You are trying to do stuff with a local Galaxy installation, and that installation is failing because you don't have the CRAN getopt package installed. I would imagine installing the missing package would be the first step, and if you have furth ...
written 5 days ago by James W. MacDonald43k
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Comment: C: convert DEseq2 R code to html
... If by 'html' you mean 'something I can read in a browser', then all this code is already 'html' at the github mirror for DESeq2. ...
written 5 days ago by James W. MacDonald43k
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Answer: A: error in the plot window of rstudio
... These are just basic R errors, and probably don't have anything to do with Bioconductor, so next time try posting at R-help (r-help@r-project.org) instead. The first error is saying that you are trying to tell R that you want your X-axis to extend to infinity (and beyond?): > plot(1:10, xlim = ...
written 6 days ago by James W. MacDonald43k
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Answer: A: Error installing org.Hs.eg.db
... R doesn't like the á in your library path. I don't know if there is a way to make R OK with that - you might google around a bit if you care - so the easiest thing to do is to use .libPaths() to set a library path that has just the base ASCII character set. ...
written 7 days ago by James W. MacDonald43k
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Comment: C: coef in dmrcate
... Right. I could translate that to be 'the column number of your design matrix that contains the coefficient you care about'. Does that make more sense? ...
written 7 days ago by James W. MacDonald43k
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Answer: A: Peaks in coverageByTranscript {GenomicFeatures}
... This function is hidden in the namespace. You could hypothetically do library(GenomicFeatures) getAnywhere(coverageByTranscript) To see the function body. An arguably better way to proceed would be to go to the GitHub mirror for this package and look at the source files. Or you could check out f ...
written 7 days ago by James W. MacDonald43k
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Answer: A: Error in dba.count
... Your sessionInfo says you are on Windows, but the directories you are specifying are what you would expect on some sort of Linux variant. You have to specify the actual correct location of your files for R to find them.   ...
written 7 days ago by James W. MacDonald43k
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Answer: A: I am trying to plot from a check box for fcs file in a reactive environment
... Shiny isn't a Bioconductor package, so this isn't the correct support forum for your question. I presume that the RStudio folks have some sort of listserv or whatnot that you could use, or perhaps you could try stackoverflow. ...
written 7 days ago by James W. MacDonald43k

Latest awards to James W. MacDonald

Teacher 4 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 4 days ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 7 days ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 20 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Scholar 5 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 5 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 6 weeks ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 6 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 9 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Cylon 9 weeks ago, received 1,000 up votes.
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Why do I get different GO term sizes using the same gene universe for 2 analyses
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
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Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 10 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Scholar 11 weeks ago, created an answer that has been accepted. For A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
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Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Converting Protein Accessions Into Protein Symbols
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