Moderator: James W. MacDonald

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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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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 10 hours 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 4 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 4 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 4 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 4 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 5 days ago by James W. MacDonald51k
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... So the first thing I do when I see something I don't understand (say, for example `clang: error: unsupported option '-fopenmp'`) is to Google the thing to see what the [Googles say about it][1]. Which brings me [to this page][2] (fourth one down), which may be relevant? I don't use MacOS, so can't ...
written 5 days ago by James W. MacDonald51k
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Answer: A: Filtering counts in SummarizedExperiment
... This isn't really a Bioconductor question, but instead is a basic 'how do I get R to do things' question. And you seem to want to do one thing, but maybe something else? I mean, do you want to filter to a minimum of 100 (really?) or something else? Anyway, you can get a long way with simple tests l ...
written 5 days ago by James W. MacDonald51k
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Comment: C: dream vignette says limma-voom repeated measures two-group comparison needs two
... Yes. If you want `lmFit` to use a mixed model you have to supply a `block` and `correlation` argument. That's just how it works (e.g., that's how you tell `lmFit` that you want a mixed model). The `voom` function is only used to estimate observation-level weights so you can use conventional linear ...
written 6 days ago by James W. MacDonald51k
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Comment: C: Applying NetAffx biological annotation to Affymetrix gene expression dataset
... You mean [like this?][1] [1]: https://cran.r-project.org/bin/linux/ubuntu/ ...
written 6 days ago by James W. MacDonald51k

Latest awards to James W. MacDonald

Scholar 10 weeks ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Limma import .gpr file error
Scholar 11 weeks ago, created an answer that has been accepted. For A: Disagreement between results of two 'getBM' queries
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Effect of lfcThreshold on p-value in DESeq2
Scholar 12 weeks 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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