User: Mike Smith

gravatar for Mike Smith
Mike Smith2.9k
Reputation:
2,910
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Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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13 hours ago
Joined:
8 years, 6 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 452 results • page 1 of 46 • next >
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Comment: C: Getting R to talk to BioMart using biomaRt
... This is because getBM is expecting a character vector, but gene_ids is a tibble. dplyr::select always returns a tibble even if you're only selecting a single column. The simplest thing to do is forget using dplyr::select and use the $ operator to extract the correct column. In the call to getBM yo ...
written 1 day ago by Mike Smith2.9k
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Comment: C: CRImage lacking functions presented in the manual
... Yes, it seems that function is missing from CRImage and the example line in the manual is simply text - it's never run or checked to see if it works. It looks like it was removed a long time ago, but you can still find it in the source code for this version of the package (http://www.bioconductor.or ...
written 5 days ago by Mike Smith2.9k
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Answer: A: Getting R to talk to BioMart using biomaRt
... Any BioMart query you can do in the browser you can also do via the biomaRt package, although I'll agree that it's not always obvious what the correct options are.  Here's a little example trying to get mouse orthologs for three fly genes we're interest in. First, lets load biomaRt and define that ...
written 6 days ago by Mike Smith2.9k
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Answer: A: Installation update of Bioconductor and R
... You're using R version 3.3.3.  That's is pretty old now, and so newer Bioconductor releases are not compatible with it.  My first suggestion would be to install the latest version of R, which is currently 3.5.1, and then either upgrade the Bioconductor packages or install them afresh. ...
written 10 days ago by Mike Smith2.9k
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Comment: C: how to find ensembl genes belonging to a GO category?
... In fairness to the OP the example does state it comes from the biomaRt vignette & fails in the same manner.   I've updated the devel vignette with the correct filter name now. ...
written 14 days ago by Mike Smith2.9k
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Comment: C: Bookdown for bioC?
... What type of vignette are you trying to make: PDF or HTML?  I'm not sure if Bioconductor would be able to handle a HTML book, as I'm not aware of any packages with multi-page HTML vignettes, but I can't see an obvious issue with a PDF produced via bookdown. Maybe you can share what you've already t ...
written 19 days ago by Mike Smith2.9k
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Comment: C: uniprot.ws install error
... The warning message is because there's a typo in your install command.  You've put 'BioGenerics' rather than 'BiocGenerics'. ...
written 28 days ago by Mike Smith2.9k
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Comment: C: "RNASeqWorkflow" package development question
... Sounds like Martin gave a fairly comprehensive answer about third-party software installation via a Bioconductor package.  Are there equivalent tools already available via existing package?  For example, rather than trying to download & compile Samtools, have you looked at using the Rsamtools pa ...
written 29 days ago by Mike Smith2.9k
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Comment: C: BiocManager::install() breaks; can't install bioc-devel
... What exactly do you mean by 'installed Bioconductor'?  Can you provide the code you ran, so if anyone else finds this post they can run it to? ...
written 5 weeks ago by Mike Smith2.9k
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Comment: C: How to handle big data sets (>10GB) in Bioconductor packages?
... Out of curiosity I thought I'd run this on a machine with 1TB of RAM to see how much is actually required.  My first comment is that I can see why you'd want to do it on a cluster, after 24hrs I've only manged to process 10% of the breast cancer dataset.  More pertinently, here's the last line of th ...
written 5 weeks ago by Mike Smith2.9k

Latest awards to Mike Smith

Scholar 5 weeks ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 9 weeks 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 5 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 5 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 15 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt is not working
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Scholar 15 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 15 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 15 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 15 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Teacher 15 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 15 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 15 months ago, created an answer that has been accepted. For A: Error in getBM of biomaRt package
Scholar 15 months ago, created an answer that has been accepted. For A: HDF5 reading speed
Scholar 15 months ago, created an answer that has been accepted. For A: hyperlink issue with a R package
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 15 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO

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