Moderator: James W. MacDonald

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14 years, 12 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: Is mapId supposed to concatenate multiVals?
... It's in the database that way: > con <- dbConnect(SQLite(), paste0(path.package("EnsDb.Mmusculus.v79"), "/extdata/EnsDb.Mmusculus.v79.sqlite")) > dbGetQuery(con, "select * from gene where gene_id='ENSMUSG00000079658';") gene_id gene_name entrezid gene_biotype gene_se ...
written 11 days ago by James W. MacDonald43k
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Answer: A: Finding DMRs using dmrFinder in bsseq
... Most of your questions could be characterized as asking how you should analyze your data. However, this support site is intended to help people with technical problems using Bioconductor software. Analyzing data is a non-trivial task, in many ways much more difficult than simply figuring out how to ...
written 11 days ago by James W. MacDonald43k
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Answer: A: read.maimages(targets, source="genepix") Error in `[.data.frame`(obj, , columns
... The arrays used for that experiment were custom one-color arrays, so you have to specify the columns by hand: > z <- read.maimages(dir(".", "^GSM"), columns = list(R = "F635 Median", Rb = "B635 Median")) Read GSM249296.gpr.gz Read GSM249524.gpr.gz Read GSM249527.gpr.gz Read GSM249529.gpr.gz ...
written 11 days ago by James W. MacDonald43k
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Answer: A: installing getgo package
... Do note that R is case sensitive, so you cannot pass 'ensgene' as an argument when the function expects 'ensGene': > supportedGeneIDs() tablename track subtrack GeneID 1 knownGene UCSC Genes <NA> Entrez Gene ID 10 vegaGene ...
written 11 days ago by James W. MacDonald43k
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Answer: A: Problem Subsetting ExpressionSet
... The phenoData slot contains information about the columns of your ExpressionSet, not the rows. ...
written 11 days ago by James W. MacDonald43k
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Answer: A: Help: extract counts from RNA-seq .bam/.bai files
... Usually I do something like library(Rsamtools) library(GenomicAlignments) bams <- dir("../", "bam$", full.names = TRUE) bfl <- BamFileList(bams, asMates = TRUE) ex <- exonsBy(TxDb.Drerio.UCSC.danRer10.refGene, "gene") ex <- reduce(ex) SE <- summarizeOverlaps(ex, bfl, singleEnd = FAL ...
written 14 days ago by James W. MacDonald43k
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Comment: C: Diff. gene expression analysis by EdgeR
... There are any number of situations that fulfill that criterion. Rather than asking an open-ended question (In what situations will I not become a millionaire?), perhaps you could say something about what you are trying to do and ask if it is workable or not. ...
written 14 days ago by James W. MacDonald43k
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Comment: C: Agilent data normalization
... For somebody other than yourself, your question is almost the same as saying that you got some data and did some stuff and it didn't work, so can somebody help? Which of course nobody can, since it's not clear at all what kind of data you have (Agilent one color or two color?), nor what you did to n ...
written 14 days ago by James W. MacDonald43k
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Comment: C: DEXSeq - Where to find and download the appropriate GTF reference file for Pytho
... Yes. > library(rtracklayer) > z <- import("Drosophila_melanogaster.BDGP5.25.62.gtf.gz") > seqlevelsStyle(z) <- "UCSC" > export(z, "tmp.gtf", "gtf") Then at a terminal prompt head Drosophila_melanogaster.BDGP5.25.62.gtf 3R protein_coding exon 380 509 . + ...
written 14 days ago by James W. MacDonald43k
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Answer: A: Change point size and remove outline in scater's plotPCA
... Rather than trying to hack things by calling ggplot2 functions directly, you might just read the help page for plotPCA, which says size_by: character string defining the column of 'pData(object)' to be used as a factor by which to define the size of points in the plot. Alternat ...
written 17 days ago by James W. MacDonald43k

Latest awards to James W. MacDonald

Teacher 10 days ago, created an answer with at least 3 up-votes. For A: Limma: Paired samples, multiple groups: problems understanding contrasts and mod
Scholar 11 days ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 28 days ago, created an answer with at least 3 up-votes. For A: Filtering absent transcripts from Gene ST array
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Can edgeR TMM normalization be used for other count data?
Scholar 4 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
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: makeOrgPackage in AnnotationForge "GID" problem
Scholar 5 weeks ago, created an answer that has been accepted. For A: makeOrgPackage in AnnotationForge "GID" problem
Scholar 7 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 9 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 9 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 10 weeks ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Scholar 3 months ago, created an answer that has been accepted. For A: edgeR on DEG analysis: Size cannot be NA nor exceed 65536
Appreciated 3 months ago, created a post with more than 5 votes. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Cylon 3 months ago, received 1,000 up votes.
Teacher 3 months 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 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Normalization factor in TMM method

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