Moderator: James W. MacDonald

Reputation:
41,850
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Location:
United States
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Google Scholar Page
Last seen:
6 hours ago
Joined:
14 years, 8 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 • 4,603 results • page 2 of 461 • next >
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Comment: C: problems filtering antigenomic probes from HTA 2.0
... OK, so don't do that. If you are over the limit of what the support site will allow you, then take the hint and cut it down to something reasonable rather than posting five separate blasts of text. Pretty much nobody has the time to read all that. Second, I told you last time to please use the ADD ...
written 5 days ago by James W. MacDonald42k
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Answer: A: Error in Gviz | IdeogramTrack
... I have committed a fix for this to both the release and devel versions of rtracklayer. As usual, these will take a day or so to propagate through the build servers. Or you can hang with the cool kids by getting the updates from subversion. ...
written 5 days ago by James W. MacDonald42k
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Comment: C: Beginner question: differences/advantages of Bioconductor for sequence analysis
... An alternate viewpoint is that as a beginner, it is in your best interest to educate yourself as to the similarities and differences between the different choices available to you and then make that choice yourself. That way you become not a beginner, and you have some idea of the capabilities that ...
written 5 days ago by James W. MacDonald42k
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Answer: A: GenomicAlignment: Import genomic intervals described in a bed file into "summari
... I think you misunderstand the code. You are defining genomic regions of interest (exons), based on the GFF file, and then you are counting up all the reads from your bamfiles that overlap these regions of interest, using summarizeOverlaps. ...
written 5 days ago by James W. MacDonald42k
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Answer: A: Why do I get different GO term sizes using the same gene universe for 2 analyses
... Please note that the GO ontology is a directed acyclic graph (DAG), which operates like a dendrogram, where lower terms are combined into higher terms. So if you have a parent term that has two child terms, then all the genes that are annotated to the two child terms are also by default annotated to ...
written 5 days ago by James W. MacDonald42k
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Comment: C: Error in Gviz | IdeogramTrack
... Why do you think that? Here's the latest from the commit log: ------------------------------------------------------------------------ r123225 | m.lawrence | 2016-11-01 10:43:43 -0700 (Tue, 01 Nov 2016) | 2 lines Changed paths: M /branches/RELEASE_3_4/madman/Rpacks/rtracklayer/DESCRIPTION M ...
written 6 days ago by James W. MacDonald42k
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Answer: A: Error in Gviz | IdeogramTrack
... This is something from rtracklayer. > rtracklayer::ucscGenomes() Error in getNodeSet(doc, "//table[@class='descTbl']")[[1L]] : subscript out of bounds Not sure if Michael Lawrence will see this thread, so I'll ping him directly. ...
written 6 days ago by James W. MacDonald42k
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Comment: C: about columm "size" in out of hyperGtest ( Gostat package)
... Trying to resurrect a thread from 7 years ago isn't the ideal way to proceed. Instead, submit a new question. Also, show code and the output from sessionInfo() ...
written 6 days ago by James W. MacDonald42k
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Comment: C: RNA degradation plot for GeneChip Mouse Gene 2.0 ST Array
... That's awesome! They don't like the RNA Integrity Number? That, like, everybody else uses? That's being a true contrarian. Anyway, you could do some sort of bootleg approximation, with emphasis on the bootleg part of that statement. First, do note that the Gene ST arrays have (in general) four prob ...
written 7 days ago by James W. MacDonald42k
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Comment: C: GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
... This error seems to be cropping up in GenomicFeatures:::.prepareBiomartMetadata, which is an internal function that isn't really intended for people to call directly. Regardless, we can call this function directly to see if we can get the error you see: > mart <- useMart("ENSEMBL_MART_ENSEMB ...
written 7 days ago by James W. MacDonald42k

Latest awards to James W. MacDonald

Scholar 1 day ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 1 day ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Cylon 5 days ago, received 1,000 up votes.
Teacher 5 days 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 5 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Teacher 11 days ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 13 days ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Scholar 21 days ago, created an answer that has been accepted. For A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
Scholar 23 days ago, created an answer that has been accepted. For A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: what is the difference between "pd.mogene.2.0.st" and "mogene20sttranscriptclust
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Concatenation of Bimap
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: featureCount - very less Successfully assigned reads
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Converting Protein Accessions Into Protein Symbols
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to deal with Affymetrix GeneChip probeids that map to multiple genes
Scholar 10 months ago, created an answer that has been accepted. For A: Converting Protein Accessions Into Protein Symbols
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: including information indicating upregulation/downregulation of genes in goana()
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: how to extract Granges not overlapping with other ganges?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Voom: estimation of mean-variance relationship with gene expression data normali
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: limma - F-test for many condition
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Interpretation of voom limma's intercept coefficient
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembl
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: TopTable Problem : Unique Adj.P.Val which is near 1
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: What is logFC and "B" in methylation analysis ??

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