User: Mike Smith

gravatar for Mike Smith
Mike Smith1.7k
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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2 hours ago
Joined:
7 years, 2 months ago
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g********@gmail.com

Posts by Mike Smith

<prev • 264 results • page 1 of 27 • next >
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Comment: C: Problem in extracting a row from matrix in rhdf5
... Hi Filipe, Thanks for reporting this.  I've managed to reproduce this with a simple example.  I'll look into why it's happening and report back once I've got a solution. ...
written 6 days ago by Mike Smith1.7k
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Answer: A: topGO gene names/ensembl IDs
... I'm afraid I can't help with the topGO part, but to retain the mapping between your query and the returned values with biomaRt, you can normally list the same variable as both an attribute and a filter.   At the moment it looks like you aren't specifying what variable you want to filter on, so the ...
written 14 days ago by Mike Smith1.7k
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Answer: A: BiomaRt xenopus tropicalis genome unavailable
... Hi Anne, I'm afraid biomaRt (the package) doesn't really work like that.  It is designed to provide a way to connect to data stores that are running BioMart (the service) as a way to query their databases.  Ensembl is by far the most widely used of these data stores, but there are many other smalle ...
written 16 days ago by Mike Smith1.7k
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Comment: C: Error with read.idat() function in illuminaio package
... Normally it's a good idea to ask a new question here, rather than adding an 'answer' to an existing one.  People are more likely to notice a new question with no answers, than bumping something old. Looking at this, the data are unusual, but it's basically the same problem as was identified before ...
written 21 days ago by Mike Smith1.7k
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Comment: C: Inconsistencies in biomart results
... No problem, this seemed like a bit of an insidious bug when I thought about it.   Let me know if it causes any issues your end.  I don't know if you ever ban IPs or anything, but if someone asks for data on 30,000 genes you'll get 60 queries in quick succession now, which might look strange in the ...
written 21 days ago by Mike Smith1.7k
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Answer: A: Inconsistencies in biomart results
... Dredging up an old post here, but I've modified the getBM() function in biomaRt to submit queries in batches if the number of values exceeds 500.  If you have multiple filters each of which have more than 500 values it should generate multiple mutually exclusive queries so that all combinations are ...
written 22 days ago by Mike Smith1.7k
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Comment: C: BiomaRt package not working
... Cool, I made my suggested substitutions based on the 'Description' field, so point out if that was incorrect. Should there still be an entry in the file for go_accession -> go_id? I can't see one, but go_accession is no longer listed as an attribute. ...
written 29 days ago by Mike Smith1.7k
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Answer: A: biomaRt error in useMart
... The main Ensembl website is down for maintenance a the moment.  If you go to it in a web browser you get redirected to a page telling you this.  The same thing happens when you run a query in biomaRt and the current release version doesn't cope very well and you get that unhelpful error message. Th ...
written 29 days ago by Mike Smith1.7k
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Answer: A: BiomaRt package not working
... Did you try using the listAttributes() function as suggested in the output message you've highlighted? As James says a new Ensembl plants has  been release, and some of the attribute names have changed.  These are documented here although I'm not sure that list is accurate since, for example, there ...
written 29 days ago by Mike Smith1.7k
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Comment: C: TCGAbiolinks Error in gene.location$ensembl_gene_id : $ operator is invalid f
... The next release of Bioconductor is scheduled for two weeks time (April 25th).  Changes to the existing release versions of the packages are now closed, and then on that date the current devel version will become a new release (which should be biomaRt v2.32.0).  All the changes I've made will be pre ...
written 6 weeks ago by Mike Smith1.7k

Latest awards to Mike Smith

Scholar 29 days ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 6 weeks ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 11 weeks ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Guru 12 weeks ago, received more than 100 upvotes.
Scholar 3 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 3 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Autobiographer 5 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 13 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Teacher 13 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
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Supporter 13 months ago, voted at least 25 times.
Scholar 13 months ago, created an answer that has been accepted. For A: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Scholar 13 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 13 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Scholar 13 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 13 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 13 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 13 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 13 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Scholar 14 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website

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