User: Mike Smith

gravatar for Mike Smith
Mike Smith2.1k
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2,100
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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23 minutes ago
Joined:
7 years, 8 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 322 results • page 1 of 33 • next >
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Answer: A: rhdf5 h5ls output differs from Linux to Windows
... Sorry for the delay in replying to this.  For future reference, on this board it's normally good practice to give the name of the package you're having issue with as one of the tags.  I get notified if there's a post tagged rhdf5 but I don't look out for the individual functions. I'm don't have a s ...
written 10 days ago by Mike Smith2.1k
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Answer: A: Identifying long stretches of Ns in hg19
... The 'masked' versions of the reference genomes (e.g. http://bioconductor.org/packages/BSgenome.Hsapiens.UCSC.hg19.masked/) come with a mask that represents the gaps in the assembly. You haven't said what you're trying to do, but you can get the locations of all the gaps on chromosome 1 by doing som ...
written 17 days ago by Mike Smith2.1k
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Comment: C: biomaRt error: Query ERROR: caught BioMart::Exception: non-BioMart die():
... The 500 values has always applied to the queries sent to BioMart, either via biomaRt or using the Ensembl web interface.  For the most part you can submit more than 500 filter values and it will be fine, but if there is a problem you won't know anything about it - it happens silently.  This is obvi ...
written 23 days ago by Mike Smith2.1k
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Comment: C: biomaRt error: Query ERROR: caught BioMart::Exception: non-BioMart die():
... Those answers are still valid, but I want to add that I don't experience the problem you're seeing, so maybe it has already been fixed at the Ensembl side. ...
written 4 weeks ago by Mike Smith2.1k
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Answer: A: biomaRt error: Query ERROR: caught BioMart::Exception: non-BioMart die():
... That's a new error to me!  I suspect that something is wrong with the back end database, rather than with the biomaRt package. One thing you can try is to use one of the mirror services, to see if that is unaffected, e.g: ensembl <- useMart("ENSEMBL_MART_ENSEMBL", dataset = ...
written 4 weeks ago by Mike Smith2.1k
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Comment: C: Illumina bead array analysis
... I think Dropbox removed support for their public folders a while back, hence the dead link.  Try here: http://www.huber.embl.de/users/msmith/beadarray/AsuragenMAQC_BeadStudioOutput.zip ...
written 5 weeks ago by Mike Smith2.1k
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Answer: A: getBM query to useEnsembl(biomart="snp"..) not responding
... This should now be fixed (https://groups.google.com/forum/?fromgroups#!topic/biomart-users/ckiglj9Og6A) ...
written 5 weeks ago by Mike Smith2.1k
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Comment: C: getBM query to useEnsembl(biomart="snp"..) not responding
... I can confirm I'm experiencing the same issues.  I see the same problem if I use one the Ensembl mirror sites, or the web interface to carry out the query, which suggests to me that it's an issue with the databae, rather than the web interface.  If that's the case then there isn't really anything we ...
written 5 weeks ago by Mike Smith2.1k
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Answer: A: Retrieving probes mapping to gene ID in microarray analysis
... How about something like this using biomaRt.  This might only be valid for the Mouse Gene ST 2.1 though, Ensembl only seem to have data for 1.0 and 2.1. library(biomaRt) ## set up biomart ensembl_mart <- useMart("ensembl") ensembl_mart <- useDataset("mmusculus_gene_ensembl", mart = ensembl_ ...
written 6 weeks ago by Mike Smith2.1k
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Comment: C: function getAE from ArrayExpress needs update because EBI has switched to https
... IMO Bernd's solution looks pretty good for minimal changes to the package code.  It just uses RCurl to read the xml into a character variable, which is then parsed with XML in the same way as before, rather than giving the URL directly. ...
written 7 weeks ago by Mike Smith2.1k

Latest awards to Mike Smith

Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: R: error while reading .h5 files from R using rdhf5 package
Appreciated 5 months ago, created a post with more than 5 votes. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 5 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 7 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 7 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 8 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Guru 9 months ago, received more than 100 upvotes.
Scholar 9 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 9 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Autobiographer 11 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 19 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 19 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 19 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Supporter 19 months ago, voted at least 25 times.
Scholar 19 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 19 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 19 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 19 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 19 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks

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