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 • 484 results • page 1 of 49 • next >
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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 5 days ago by Mike Smith3.1k
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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 5 days ago by Mike Smith3.1k
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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 8 days ago by Mike Smith3.1k
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Comment: C: arrayQualityMetrics in reading HTAfeatureSet read by oligo package
... Is it possible for you to save data using the save() function and then share that ExpressionSet object so I can try and debug? I've not seen this error message before. ...
written 8 days ago by Mike Smith3.1k
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Comment: C: Biomart cannot get multiple genes?
... Great glad it makes sense.  Depending what you're trying to do, you can either use the mmusculus_gene_ensembl dataset if you want to annotate the mouse genes, or take a look at the getLDS() function if you want to find matches across species. ...
written 15 days ago by Mike Smith3.1k
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Answer: C: Biomart cannot get multiple genes?
... I still think this might be a case sensitive issue.  The lines I've reproduced below show that there are multiple values returned by your query. It's not the full 1000, but 697 gene symbols are matched by your query. > length(Info$hgnc_symbol) [1] 697 > length(mca_filter) [1] 1000 It is no ...
written 16 days ago by Mike Smith3.1k
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Comment: C: Biomart cannot get multiple genes?
... Before digging any deeper, can you check this isn't due to case sensitive matching.  The command which(Info$hgnc_symbol == "Selenop") will only match entries that look like Selenop, but your query returns SELENOP.   Your first example will fail this too: Info <- getBM(attributes = attr, ...
written 16 days ago by Mike Smith3.1k
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Comment: C: biomaRt: Ensembl -> Entrez conversion error?
... I'm afraid it's a property of BioMart - the database system used to serve up the Ensembl data.  It's not something I can fix in the R package; if you run the same query in the Ensembl BioMart web interface it will silently drop empty results there too. As James mentioned, the safest thing to do is ...
written 18 days ago by Mike Smith3.1k
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Answer: A: biomaRt: Ensembl -> Entrez conversion error?
... Thanks for the example code, but I don't see this behaviour when I try to run your query. I think the example below is doing the same thing, but only using the two Ensembl IDs you mention, and I get back different Entrez IDs to you. library(biomaRt) ## Use mouse genes mart mart <- useMart("ense ...
written 18 days ago by Mike Smith3.1k
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Comment: C: Rhdf5lib install problems
... Thanks for the report, I'm not immediately sure what the issue is here, but I'll look into it.  Can you just confirm that the following command produces the same error for you - this work for me on Linux Mint 18 with R-3.5.1 install.packages('https://bioconductor.org/packages/3.8/bioc/src/contrib/ ...
written 22 days ago by Mike Smith3.1k

Latest awards to Mike Smith

Scholar 6 weeks ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 6 weeks ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 10 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 10 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 7 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 7 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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