Moderator: James W. MacDonald

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United States
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Joined:
16 years, 4 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

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Answer: A: How to convert CEL data to Bed/Bim/Fam/VCF for plink
... In general you would process the celfiles using the crlmm package. There are several vignettes for that package that you could read. As for converting the calls to Plink compatible format, that's something you could use the GWASTools package to do. ...
written 1 day ago by James W. MacDonald48k
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Answer: A: Problem for finding "Locus Link ID" from Annotation file
... Although often asked about around here, WGCNA isn't actually a Bioconductor package. It's a CRAN package. Questions about CRAN packages should be asked at R-help@r-project.org. Your main problem is that you are following a tutorial without understanding it enough to apply to your own data. The basi ...
written 1 day ago by James W. MacDonald48k
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Comment: C: How to find overlaps in genomic sequences comparing patients to themselves
... Can you expand on this? How are the overlapping regions on the same patient not all the same regions? Or do you have two GRanges for each patient? If the latter, why not just use findOverlaps? ...
written 3 days ago by James W. MacDonald48k
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Answer: A: Merge column to SummarizedExperiment from other dataframe
... When you merge the colData and your data.frame you end up changing the rownames of the resulting DataFrame, which is where the colnames come from. You could just do cn <- colnames(aems450k1.MvaluesQCIMPplaqueSE) colData(aems450k1.MvaluesQCIMPplaqueSE) <- merge(colData(aems450k1.MvaluesQCIMP ...
written 3 days ago by James W. MacDonald48k
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Comment: C: Preparation of summarizedExperiment for dexSeq
... You should probably include the output from both traceback() and sessionInfo() (in that order) after you get the error. ...
written 4 days ago by James W. MacDonald48k
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Answer: A: Can not install MINFI in WinDow 10 correctly
... Any time you see an error like there is no package called 'GenomeInfoDbData' That is intended to be informative, and means that you are missing a package called GenomeInfoDbData. The cure for that error is to install biocLite("GenomeInfoDbData") and then go back and try to install minfi again ...
written 4 days ago by James W. MacDonald48k
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Answer: A: NCBI hg38 transcript annotation package GenomicFeatures
... library(BiocInstaller) biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene") If you use makeTxDbFromBiomart, you get a TxDb based on EBI/EMBL mappings, which is not the same as NCBI. UCSC is technically not the same either, but it is very close, and one could argue a bit cleaner. ...
written 4 days ago by James W. MacDonald48k
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Answer: A: Limma Volcano Plot Highlight Top Genes by Color
... You can just add your own, using the points function. volcanoplot(fit2,coef="Diff.1", names=fit$genes$NAME, main="mDC vs iDC") lp <- -log10(fit2$p.value[,"Diff.1"]) ord <- order(lp, decreasing = TRUE)[1:10] points(fit2$coef[ord,"Diff.1"], lp[ord], pch = 16, cex = 0.45, col = 2) ...
written 8 days ago by James W. MacDonald48k
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Comment: C: Subscript error from TSS proximity function
... Yes. Is getNearestDist a function in S4Vectors? ...
written 8 days ago by James W. MacDonald48k
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Comment: C: Subscript error from TSS proximity function
... Hello rbronste! We believe that this post does not fit the main topic of this site. This support site is for Bioconductor packages, not for help debugging your own code. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can hel ...
written 8 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: BiomaRt returns 0 obs
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: EdgeR blocking and "All combinations of multiple factors"
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
Teacher 6 weeks 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 6 weeks ago, created an answer that has been accepted. For A: goseq: Formatting category list for use with goseq
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
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. 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: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Retrieving all genes related a go term
Scholar 10 weeks ago, created an answer that has been accepted. For A: Error in .checkKeys(value, Lkeys(x), x@ifnotfound) : value for "GO:0000059" not
Scholar 10 weeks ago, created an answer that has been accepted. For A: BiomaRt returns 0 obs
Scholar 10 weeks ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Scholar 10 weeks ago, created an answer that has been accepted. For A: Bioconductor: quantile normalization
Scholar 10 weeks ago, created an answer that has been accepted. For A: Retrieving all genes related a go term
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to export enrichGO results for future visualization with barplot, dotplot, e
Scholar 10 weeks ago, created an answer that has been accepted. For A: How does edgeR cpm function calculate log(CPM) values?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: How to export enrichGO results for future visualization with barplot, dotplot, e
Teacher 10 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 10 weeks ago, created an answer that has been accepted. For A: Why so many entries are 'not mapped' in ragene20sttranscriptcluster.db?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Popular Question 4 months ago, created a question with more than 1,000 views. For GEOquery error
Appreciated 4 months ago, created a post with more than 5 votes. For A: Best way to convert uniprot accessions to entrez gene identifiers in R

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