Moderator: James W. MacDonald

Reputation:
48,290
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United States
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Google Scholar Page
Last seen:
2 days, 7 hours ago
Joined:
16 years, 6 months ago
Email:
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 • 5,606 results • page 2 of 561 • next >
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Answer: A: Normalization for small non-coding RNA and multi-factor design
... Your question could be re-stated (uncharitably, perhaps) as 'How should I analyze my data?', which is in general beyond the scope of this support page, which is intended primarily to help people with technical aspects of using Bioconductor software. Do note that anybody can post an answer on this s ...
written 5 days ago by James W. MacDonald48k
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Answer: A: Multi-sample Heatmap from GRange
... You should probably use Gviz for that. See the vignette and help page for DataTrack. ...
written 5 days ago by James W. MacDonald48k
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Answer: A: GDCprepare stop working for some unknown reason
... The function you are using is intended to download and prepare the data, and then save it in an R object. If you call that function again, it will download and prepare the data, as advertised. If you want to use the file that you have prepared, you load it into your workspace and then use it. ...
written 6 days ago by James W. MacDonald48k
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Answer: A: plot get overridden rather to overlapped
... This has nothing to do with any Bioconductor package, but instead is a question about base R (or more correctly your own code). You could ask on R-help (r-help@r-project.org), or you could do a Google search for something like 'multiple lines R plot', or you could look at the code for say plotDensit ...
written 6 days ago by James W. MacDonald48k
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Answer: A: benefits of pearson distance for hierarchical clustering
... You can make an argument that correlation (or 1-cor) is a better distance measure for a couple of reasons. First, the intensity and range gene expression measures are to a certain extent dependent on either the length (for RNA-Seq) or GC content (for microarrays), and if you use Euclidean distance y ...
written 6 days ago by James W. MacDonald48k
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Comment: C: minfi R package for methylation analysis of infinium 450K microarray data
... I keep telling you how to resolve it. The error is telling you that the directory you are pointing to does not exist! If you tell R to read something from a non-existent directory, you shouldn't be surprised if it says that it doesn't exist. As an example: > dir.does.not.exist <- "C:/this/is/ ...
written 10 days ago by James W. MacDonald48k
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Comment: C: minfi R package for methylation analysis of infinium 450K microarray data
... Well I have no idea what baseDir might be, so how could I possibly help? And I already answered your question - perhaps you need to re-read my original answer? And as a hint - remove the extra slash at the beginning of the path to your sample sheet.   ...
written 10 days ago by James W. MacDonald48k
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Comment: C: how to retrieve all attributes from biomart ?
... Oh, you mean gene ontology, not onthology. Fair enough. And if you prefer to do it your own way, rather than using the existing packages to do so, I guess you should have at it. But do note that doing things 'your own way' implies that you A) know what you are doing, and B) have it handled. So good ...
written 10 days ago by James W. MacDonald48k
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Comment: C: how to retrieve all attributes from biomart ?
... What is gene onthology? ...
written 10 days ago by James W. MacDonald48k
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Comment: C: make TxDb from list of genes
... Why do you want a TxDb for just a set of genes? It's simple enough to use a full sized one and subset after the fact. ...
written 10 days ago by James W. MacDonald48k

Latest awards to James W. MacDonald

Scholar 6 weeks ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Have troubles with finding Annotations for Bovine and Rhesus\' platforms
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Probe to gene id conversion
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
Scholar 6 weeks ago, created an answer that has been accepted. For A: BiomaRt returns 0 obs
Scholar 6 weeks ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 6 weeks ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Scholar 11 weeks ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Scholar 11 weeks ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Scholar 11 weeks ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 3 months ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Scholar 3 months ago, created an answer that has been accepted. For A: BiomaRt returns 0 obs
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Retrieving all genes related a go term
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: EdgeR blocking and "All combinations of multiple factors"
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: Why the log fold change of some genes returned by edgeR is not compatible with t
Scholar 3 months ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Scholar 3 months ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: How to export enrichGO results for future visualization with barplot, dotplot, e
Scholar 4 months ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Scholar 4 months ago, created an answer that has been accepted. For A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not

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