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User: Mike Smith

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Mike Smith3.2k
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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 • 501 results • page 2 of 51 • next >
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Answer: A: biomaRt bug report
... These a couple of points to address here. The first is that because the **biomaRt** package is accessing Ensembl's BioMart, which gets updated every 3 months, it's quite likely that the results of examples you find in tutorials or slides will no long match. This is because the underlying database h ...
written 26 days ago by Mike Smith3.2k
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Comment: C: biomaRt: Unexpected format to the list of available marts.
... More often that not this error occurs when Ensembl is down for maintenance, and all requests get redirected to a status page. Thus you don't get any sort of HTTP error to detect, so asking a user to open the link is a quick way for them to determine what the issue is. However, this clearly isn't ...
written 4 weeks ago by Mike Smith3.2k
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Comment: C: biomaRt: Unexpected format to the list of available marts.
... This is odd, because you're getting the correct result in the browser, so it isn't a fundamental connection problem either at your end or with Ensembl. Your code also works fine for me. You could try using one of the mirror sites e.g. ```r mart <- useEnsembl('ensembl', mirror = 'useast') ``` ...
written 4 weeks ago by Mike Smith3.2k
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Answer: A: biomarRt for fungi
... You should still be able to access the Ensembl Fungi data using **biomaRt**. Does this work for you? ```r library(biomaRt) ensembl_fungi <- useMart(host="https://fungi.ensembl.org", biomart="fungi_mart", port = 443) head(listDatasets(ensembl_f ...
written 5 weeks ago by Mike Smith3.2k
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Answer: A: Is biomaRt down?
... Did you try visiting the page suggested in the error message?  Did it go anywhere, or time out? The main Ensembl site seemed to be very slow yesterday.  There are several mirror that you can try using if the main site isn't working.  You can elect to use these with: mart <- useEnsembl(biomart ...
written 5 weeks ago by Mike Smith3.2k
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Comment: C: Invalid result from biomaRt
... That function has actually been there for years, but was very rarely used in examples or documentation.  Since 99% of the biomaRt questions are related to Ensembl, I thought I would start making it more visible.  I find the mirror argument easier to remember than typing in the alternative URLs, hope ...
written 5 weeks ago by Mike Smith3.2k
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Answer: C: Invalid result from biomaRt
... The main Ensembl site seems to be very slow for me at the moment.  I can't even get the useMart() step to work reliably. Do you get the same behaviour if you try a mirror? e.g. mart <- useEnsembl("ensembl","sscrofa_gene_ensembl", mirror = 'uswest') ...
written 5 weeks ago by Mike Smith3.2k
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Comment: C: Biostrings: revComp error: Not compatible with STRSXP
... You have a lot more packages loaded in the second session, and I would guess that one of these has functions called complement and reverseComplement and these are over-riding the versions present in Biostrings. You could take a look at the conflicted package (https://conflicted.r-lib.org/) which tr ...
written 9 weeks ago by Mike Smith3.2k
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Answer: A: arrayQualityMetrics in reading HTAfeatureSet read by oligo package
... I think this is because you have the @ symbol in your file names. arrayQualityMetrics has templates for the reports it produces, with the structure indicated by placeholder entries like @ARRAYNAME@. These are then replaced by the values in the expressionSet when the report is produced. It's getting ...
written 9 weeks ago by Mike Smith3.2k
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Comment: C: Problem installing scater
... Not answering your question, but I just wanted to point out you can use the pattern argument to filter the results you get from BiocManager::available(), so you don't have to look through the entire list e.g. > BiocManager::available(pattern = "scate") [1] "scater" ...
written 10 weeks ago by Mike Smith3.2k

Latest awards to Mike Smith

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: getBM error: The query to the BioMart webservice returned an invalid result
Scholar 10 weeks ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 3 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 3 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 4 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 4 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 5 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 8 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 9 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 9 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 19 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 19 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 19 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 19 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 19 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 19 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 19 months ago, created an answer that has been accepted. For A: biomaRt is not working
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 19 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 19 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 19 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names

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