User: Mike Smith

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Mike Smith3.1k
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EMBL Heidelberg / de.NBI
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http://www.msmith.de/
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Posts by Mike Smith

<prev • 482 results • page 2 of 49 • next >
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Answer: A: EBImage computeFeatures error
... I can't reproduce this error at the moment.  I've made a modified version of your example script available at https://gist.github.com/grimbough/09d150bff2b07ec032de4d47cf201215 The main changes were to remove all the comment out lines so it was easier for me to read, automated the downloading & ...
written 20 days ago by Mike Smith3.1k
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Comment: C: EBImage computeFeatures error
... Can you update your post to include the output of the command sessionInfo(), so we can see the exact versions you're using. I've don't get this error when I run through your script (with a few changes to fix the plate number to 2). ...
written 20 days ago by Mike Smith3.1k
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Answer: A: Functions listFilterValues and searchFilterValues are not working in biomaRt
... These functions a very new, so they've only been added to the developmental version of biomaRt for now (specifically a version >= 2.39.2).  If you want to try them out you can either follow the installation instructions at https://www.bioconductor.org/packages/devel/bioc/html/biomaRt.html (you'll ...
written 25 days ago by Mike Smith3.1k
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Answer: A: biomaRt error message
... I think this error is because when you go to archive.plants.ensembl.org you are actually redirected to mar2016-plants.ensembl.org and biomaRt doesn't cope with this redirection. However if you use the correct URL in your R query you currently encounter a different error. I get this same error when ...
written 4 weeks ago by Mike Smith3.1k
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Comment: C: Problem with apostrophe in biomaRt query
... biomaRt version 2.39.2 now contain the functions listFilterValues and searchFilterValues. You can use these to try and determine the appropriate values to supply to a filter like phenotype_description. Here's an example of how they work: ## Use the Ensembl human SNP dataset ensembl <- useEnsemb ...
written 4 weeks ago by Mike Smith3.1k
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Answer: A: Problem with apostrophe in biomaRt query
... Thanks for reporting this.  There's actually a couple of different things going on here. First, you're absolutely right that the apostrophe is breaking the query. biomaRt uses apostrophes to separate the values when it submits the query, so sticking an extra one in leaves a mismatch and causes the ...
written 4 weeks ago by Mike Smith3.1k
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Comment: C: dmrseq installation failed
... Just as a follow up, I believe the Github repo is at https://github.com/rafalab/bumphunter and you can install directly from there via: BiocManager::install('rafalab/bumphunter') ...
written 4 weeks ago by Mike Smith3.1k
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Answer: A: biomaRt question (missing gene information?)
... If you search Ensembl for CPSF3L you'll find you get directed to the page for INTS11, and CPSF3L is listed as a Gene Synonym.  The exact reason for this isn't given but usually this is because the old name has been retired, or two entries have been merged together sometime in the past. Unfortunatel ...
written 5 weeks ago by Mike Smith3.1k
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Answer: A: Can't push upstream - duplicate commits
... This support forum is principally intended for user questions. For package development & maintainance help please use the Developer Mailing list at https://stat.ethz.ch/mailman/listinfo/bioc-devel You'll get a more rapid response to git related issues there. ...
written 5 weeks ago by Mike Smith3.1k
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Comment: C: Getting gene symbols with ensemble ids and mstrg ids
... You're more likely to get a helpful response if you include a small example of what you're trying to do e.g. if biomaRt didn't achieve the result you want show this with some code.  That way others here can try to run your example to help diagnose the issue or suggest a solution. ...
written 6 weeks ago by Mike Smith3.1k

Latest awards to Mike Smith

Scholar 5 weeks ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 5 weeks ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 3 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 4 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 6 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 6 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 17 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 17 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 17 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 17 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 17 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 17 months ago, created an answer that has been accepted. For A: biomaRt is not working
Scholar 17 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 17 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 17 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Scholar 17 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 17 months ago, created an answer that has been accepted. For A: Error in getBM of biomaRt package

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