User: Mike Smith

gravatar for Mike Smith
Mike Smith1.9k
Reputation:
1,900
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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5 hours ago
Joined:
7 years, 4 months ago
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g********@gmail.com

Posts by Mike Smith

<prev • 288 results • page 1 of 29 • next >
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Answer: A: biomaRt: list of hosts accessed
... You're correct that the host name is not hard coded into the package (at least it shouldn't be).  biomaRt (the R package) is designed as a tool to access any server that is running BioMart (the service) to provide access to its data.  The host argument is used to specify this in most functions.  Ens ...
written 1 day ago by Mike Smith1.9k
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Comment: C: Please use the function 'listAttributes' to get valid attribute names
... Not easily is the short answer.  Ensembl usually list them in their release notes e.g. ftp://ftp.ensembl.org/pub/release-88/release_88_biomart_changes.txt and Thomas Maurel generally mentions them in his Ensembl release posts here (https://support.bioconductor.org/p/94329/), but normally I find out ...
written 3 days ago by Mike Smith1.9k
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Comment: C: arrayQualityMetrics: "All SVG style attribute must have length 1" and other erro
... Hi, When I run your example code I actually get a different error: Error in file.info(x) : invalid filename argument If I then run it again I then see Only one 'gridsvg' device may be used at a time which is presumably because it didn't close the device properly during the first run.  Can you ...
written 3 days ago by Mike Smith1.9k
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Answer: A: Please use the function 'listAttributes' to get valid attribute names
... The error message tries to give you some hints as to what to do next: Invalid attribute(s): uniprot_swissprot, uniprot_genename Please use the function 'listAttributes' to get valid attribute names The first line above tells you that both uniprot_swissprot and uniprot_genename are invalid attr ...
written 3 days ago by Mike Smith1.9k
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Answer: A: Rsubread install problems on CentOS 6.8/R3.4.1/gcc/4.8.2
... The ifreq struct should be defined in <net/if.h>, which for me is found in /usr/include/.  Is it present on your system, and included during compilation?   ...
written 5 days ago by Mike Smith1.9k
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Answer: A: Unable to install the package "tissuesGeneExpression"
... I'm not sure the tissuesGeneExpression package was ever 'officially' in Bioconductor, I think it was created for teaching purposes only.  You can find a Github repository for it at https://github.com/genomicsclass/tissuesGeneExpression and you can try installing it form there using this code: libr ...
written 6 days ago by Mike Smith1.9k
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Answer: A: biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id
... I think this is probably related to a problem the Ensembl BioMart has when your list of query values is very long.  You'll notice on the web interface it only recommends submitting up to 500 values at a time.  If you submit something longer than this the query may time out, but it does so silently a ...
written 7 days ago by Mike Smith1.9k
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Comment: C: biomaRt Ensembl ID query returns NA in 'ensembl_gene_id', 'ensembl_transcript_id
... Can you provide the output from sessionInfo() so we can see which version of biomaRt you're using?   ...
written 8 days ago by Mike Smith1.9k
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Comment: C: Unable to install package curatedMetagenomicData using R 3.3.1
... Can you update your post to include the outputs from sessionInfo() and BiocInstaller::isDevel()?  The very latest version of curatedMetagenomicData requires R 3.4.0, so it maybe you're trying to install that without realising it. ...
written 13 days ago by Mike Smith1.9k
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Answer: A: legend with gradient in ComplexHeatmap
... You can do this with the heatmap_legend_param argument.  First we'll create a heatmap with the example from the ComplexHeatmap vignette: library(ComplexHeatmap) library(circlize) set.seed(123) mat = cbind(rbind(matrix(rnorm(16, -1), 4), matrix(rnorm(32, 1), 8)), rbind(matrix(rnorm(24 ...
written 15 days ago by Mike Smith1.9k

Latest awards to Mike Smith

Good Answer 28 days 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 29 days ago, created a post with more than 5 votes. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 4 weeks ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 12 weeks ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
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"
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 4 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Guru 4 months ago, received more than 100 upvotes.
Scholar 5 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 5 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Autobiographer 7 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 15 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 15 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 15 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Supporter 15 months ago, voted at least 25 times.
Scholar 15 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 15 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 15 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 15 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 15 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks

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