Moderator: James W. MacDonald

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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 • 6,005 results • page 2 of 601 • next >
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Comment: C: "adding gene annotations" in edgeR doesn't work with select()
... I should also note that `mgi_symbol` worked, but that was probably happenstance. I know from long experience that what you really want are the `external_gene_name`, but that's not what you would naively search for. ``` > getBM(c("external_gene_name","ensembl_gene_id", "mgi_symbol"), "ensembl_gen ...
written 5 days ago by James W. MacDonald51k
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Answer: A: "adding gene annotations" in edgeR doesn't work with select()
... It's not clear if you know this or not, but those are Ensembl gene IDs for Chinese hamster. The annotation package you are trying to use is for Humans, which you are aware of, and the fact that there is an 'eg' in the name is intended to indicate that the central key for the underlying database is E ...
written 5 days ago by James W. MacDonald51k
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Comment: C: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... 1. What exactly are you asking? Comment how? 2. There is a [FAQ][1]. [1]: http://genome.ucsc.edu/FAQ/FAQreleases.html ...
written 6 days ago by James W. MacDonald51k
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Answer: A: TxDb.Hsapiens.UCSC.hg38.ensGene doesn't exist
... There [isn't an ensGene table for hg38][1]. If you hit the Track dropdown, you won't see an Ensembl Track. If you change to hg37, it's there. And you should probably not use UCSC data for Ensembl anyway. Although both UCSC and Ensembl start with the GRCh38 genome, they use different pipelines to sa ...
written 6 days ago by James W. MacDonald51k
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Comment: C: BioMart does not find mouse homologs of human genes
... There's no such thing. NCBI probably has a pretty good rationale for why they think MIR155HG and Mir155hg are orthologs, and I would bet EBI/EMBL has a good rationale for why they think they aren't. And I would also bet that their rationales hinge on pretty subtle, sophisticated points where reasona ...
written 7 days ago by James W. MacDonald51k
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Comment: C: BioMart does not find mouse homologs of human genes
... If you look at the link you show above, clicking on orthologs, it says there aren't any human orthologs for that miRNA! The only orthologs are for three other mice species. This is what Mike Smith pointed out. And if you look at the link for [MIR155HG][1], the orthologs link isn't available, which I ...
written 11 days ago by James W. MacDonald51k
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Comment: C: Error in creating BSGenome package
... When you make a `BSgenome` package, you are generating everything required for the package installation in your working directory. Like an actual directory called BSgenome.Slycopersicum.SGN.SL3.00, that contains a bunch of subdirectories and whatnot. You can then install that package and use it. Pre ...
written 11 days ago by James W. MacDonald51k
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Answer: A: Error in creating BSGenome package
... So there's three parts to that error message. The first part tells you what function had the error ``` Error in Biobase::createPackage(x@Package, destdir, template_path, symvals) : ``` And the second part explains what the problem is ``` directory './BSgenome.Slycopersicum.SGN.SL3.00' exists ``` A ...
written 11 days ago by James W. MacDonald51k
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Answer: A: BioMart does not find mouse homologs of human genes
... The biomaRt package is simply a way to programmatically access the Biomart server and get the results back into R. As such, anything like this is really a Biomart issue, not biomaRt (or Bioconductor, really). Anyway, [there is a FAQ][1] [1]: http://useast.ensembl.org/Help/Faq?id=476 ...
written 12 days ago by James W. MacDonald51k
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Answer: A: Illumina 450K quality controls with meffil
... While Meffil uses some Bioconductor packages, it is not a Bioconductor package. This support site is intended for Bioc packages, not general questions. Plus as Kevin Blighe noted, cross-posting is considered bad form. For a GitHub package you should probably contact the maintainer directly rather th ...
written 12 days ago by James W. MacDonald51k

Latest awards to James W. MacDonald

Scholar 11 weeks ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 12 weeks ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Scholar 3 months ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Scholar 9 months ago, created an answer that has been accepted. For A: Limma import .gpr file error
Scholar 9 months ago, created an answer that has been accepted. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Popular Question 9 months ago, created a question with more than 1,000 views. For Saving/loading TxDb objects
Appreciated 9 months ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 9 months ago, created an answer that has been accepted. For A: limma - blocking or regressing out nuisance variable
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 9 months ago, created an answer that has been accepted. For A: Iterate through sever annotation database packages
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Scholar 9 months ago, created an answer that has been accepted. For A: Probe to gene id conversion
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 9 months ago, created an answer that has been accepted. For A: blastn for selected database and/or organism
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: DE genes comparison of different treatments from microarray and RNAseq data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Different annotation obtained from hgu133a2.db and affymetrix annotation release
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Effect of lfcThreshold on p-value in DESeq2
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How to add my own Entrez Gene IDs rather than using the ones from a default pack
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: Best method/package for Gene Set Enrichment Analysis in microarrays?
Scholar 9 months ago, created an answer that has been accepted. For A: Problems with "exonsBy" function from GenomicFeatures package

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