User: Mike Smith

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Mike Smith1.3k
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Posts by Mike Smith

<prev • 198 results • page 1 of 20 • next >
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Comment: C: adding attributes affects number of results returned
... Awesome, that looks like a result that is much more consistent with how it works with other combinations of variables.  Thanks very much. ...
written 2 days ago by Mike Smith1.3k
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Answer: A: getBM functtion in biomaRt pacakge
... I have committed a patch which should hopefully stop this problem occurring in the future.  It should be available from biomaRt version 2.31.4. The correct column names will be assigned to the results, and the column order should now always match the ordering of the attributes as they were requeste ...
written 6 days ago by Mike Smith1.3k
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Comment: C: adding attributes affects number of results returned
... Cool, glad what I've said make sense.  I've no idea how the various ensembl interfaces reference the data, but I note that there's no phenotype data available on the standard page for the SNP either (rs368991480).  The link on the left side is simply greyed out. I'll have a look at the biomaRt code ...
written 7 days ago by Mike Smith1.3k
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Comment: C: adding attributes affects number of results returned
... Hi Thomas,  Thanks for looking into this.  The example I gave doesn't try to join two datasets at all.  It's working exclusively in the Human Short Variants dataset.  From attributes I'm selecting  refsnp_id and ensembl_gene_stable_id as you've done.  I then also tick VARIANT ASSOCIATED INFORMATION ...
written 7 days ago by Mike Smith1.3k
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Answer: A: adding attributes affects number of results returned
... I've had a more detailed look at this, and I don't think the issues are to do with selecting attributes from different pages or datasets.  To me it more seems that when the underlying ensembl database contains no phenotypic information associated with a SNP, Biomart simply doesn't return anything fo ...
written 7 days ago by Mike Smith1.3k
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Answer: A: IONiseR readFast5Summary Error H5Aopen(gid, "num_events")
... Dear Christophe, Thanks for your question.  Providing access to the fast5 file is very helpful.  I've got a couple of questions that may help get IONiseR into a state that can read it.  Looking at it's contents, it formatted in a subtle different way to any to any fast5 files I've encountered befor ...
written 8 days ago by Mike Smith1.3k
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Comment: C: adding attributes affects number of results returned
... Thank you both for looking into this.  James' suggestion of trying the query on the Ensembl web interface is exactly how I debug a lot of the issues that get reported.  At the moment I find it much easier than trying to process the interim pages returned by the biomaRt code. I'll take a look at the ...
written 8 days ago by Mike Smith1.3k
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Answer: A: getBM functtion in biomaRt pacakge
... I agree this is strange behavior.  As a temporary fix you can try with the argument bmHeader = TRUE. This will use the plain text description of the field, rather than its ID.  e.g. seq<-getBM(filter="ensembl_gene_id", values="ENSMUSG00000000103", attributes=c("ensembl_tra ...
written 23 days ago by Mike Smith1.3k • updated 22 days ago by Wolfgang Huber12k
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Answer: A: biomaRT GO-ID retreival showing different genes than AmiGO
... This isn't a problem with the biomaRt package per se, as you get back the same values you find via accessing Ensembl biomart directly.   My instinct is that this query will return any gene that is directly annotated with that GO category.  It won't find anything assigned to a child category.  Is th ...
written 5 weeks ago by Mike Smith1.3k
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Comment: C: beadarray error importing from GEOquery
... What are you planning to do with the object?  Does it actually need to be a ExpressionSetIllumina?  validObject() is failing for very similar reasons to the first error, namely that dimension checks in Biobase aren't actually appropriate for the ExpressionSetIllumina class. It's been a long time si ...
written 5 weeks ago by Mike Smith1.3k

Latest awards to Mike Smith

Scholar 9 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Scholar 10 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Scholar 11 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Centurion 11 months ago, created 100 posts.
Scholar 11 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Scholar 12 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Scholar 15 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Intergenic coordinates with Genomic Feaures
Scholar 22 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures

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