User: Mike Smith

gravatar for Mike Smith
Mike Smith2.7k
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EMBL Heidelberg / de.NBI
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http://www.msmith.de/
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2 days, 15 hours ago
Joined:
8 years, 3 months ago
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Posts by Mike Smith

<prev • 425 results • page 1 of 43 • next >
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Answer: A: TCGA biomart conversion
... Here's an example of doing the conversion using biomaRt. You can use the versioned IDs you've got, but you'll see it's better the remove the version numbers. First, we'll load biomaRt and use your example IDs. library(biomaRt) mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl" ...
written 6 days ago by Mike Smith2.7k
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Comment: C: Genes listed in GO categories
... Thanks for the comprehensive answer.  I didn't appreciate that under the hood the core relationship is always GOTerm-to-EntrezID and that the will always be another mapping required for Gene IDs from any other annotation. ...
written 10 days ago by Mike Smith2.7k
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Comment: C: Genes listed in GO categories
... I totally agree with your point about different sources providing quite distinct annotations, but are those two scenarios really comparing different gene IDs?  I don't know much about the goseq functions, but both examples provide the argument 'ensGene' which implies using the Ensembl IDs in both in ...
written 11 days ago by Mike Smith2.7k
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Answer: A: Rhdf5 C-library out of date
... I'm afraid the short answer is no.  At the moment rhdf5 is bundled with HDF5 1.8.19 and you can't override that.  This is a specific design decision so that anyone relying on rhdf5 does't have to worry about supporting a myriad of HDF5 versions across multiple platforms - which is the situation if y ...
written 12 days ago by Mike Smith2.7k
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Comment: C: biomaRt - getBM() taking longer to run than usual ?
... How old was your previous version?  Did it used to print the 'batch submitting' message?  The previous versions that didn't use the batch submission method where faster, but had a tendency to silently drop results when you queried for more than 500 values at a time. ...
written 17 days ago by Mike Smith2.7k
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Answer: A: Does BiocWorkflowTools package generate F1000Reseach/Bioconductor-stype PDF at o
... The original aim of the F1000 template was primarily to make writing and submitting workflow documents easier (https://www.bioconductor.org/developers/how-to/workflows/), where the intention is to send an F1000 style document to the journal, and have a BioC style HTML available via the Bioconductor ...
written 22 days ago by Mike Smith2.7k
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Answer: A: Unable to install BiocStyle: not available (for R version 3.5.0)
... If you already have packages installed, there should be no need to install them again.  You can just load them with library() e.g. library(BiocStyle) If you do need to install a new package, it's a more typical use case to install Bioconductor packages with biocLite(). Do you get the same errors ...
written 28 days ago by Mike Smith2.7k
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Comment: C: biomaRt inconsistent errors with hsapiens_gene_ensembl
... Sounds like you're experiencing the issue described in https://support.bioconductor.org/p/104025/ This was caused by the Ensembl release at that time including some species with apostrophes in their name for the first time, which broke listDatasets(). I suggest updating your version of biomaRt to ...
written 29 days ago by Mike Smith2.7k
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Answer: A: BiomaRt - hsapiens dataset from Ensembl_Mart_Ensembl not recognised by R
... James is totally correct that you've got a typo in the dataset name, but I also wonder if you're experiencing the issue described in https://support.bioconductor.org/p/104025/ which would produce a similar error. This was caused by the Ensembl release at that time including some species with apostr ...
written 29 days ago by Mike Smith2.7k
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Answer: A: cannot reproduce biomaRt vignette
... Sounds like you're experiencing the issue described in https://support.bioconductor.org/p/104025/ This was caused by the Ensembl release at that time including some species with apostrophes in their name for the first time, which broke listDatasets(). I suggest updating your version of biomaRt to ...
written 4 weeks ago by Mike Smith2.7k

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
Teacher 5 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
Scholar 11 months ago, created an answer that has been accepted. For A: biomaRt is not working
Scholar 11 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 11 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 11 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 11 months ago, created an answer that has been accepted. For A: hyperlink issue with a R package
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 11 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 11 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Scholar 11 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 11 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 11 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Teacher 11 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
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 11 months ago, created an answer that has been accepted. For A: Get cytoband from refsnp ID using biomaRt in R
Scholar 11 months ago, created an answer that has been accepted. For A: HDF5 reading speed
Scholar 11 months ago, created an answer that has been accepted. For A: Error in getBM of biomaRt package
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 11 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Scholar 11 months ago, created an answer that has been accepted. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 11 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?

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