User: Mike Smith

gravatar for Mike Smith
Mike Smith2.5k
Reputation:
2,510
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
23 hours ago
Joined:
7 years, 11 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 376 results • page 2 of 38 • next >
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Comment: C: HDF5 reading speed
... Thanks for the follow up with your data I'll take a look at it in the next few days and try to offer some insight.  I just did some testing with the code below to read a 'large' integer matrix where rhdf5 seemed to be quicker, so there's definitely a few things to look at.  This is with the devel ve ...
written 10 days ago by Mike Smith2.5k
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Answer: A: HDF5 reading speed
... Interesting question, I've never really compared the various HDF5 reading packages against each other.  Since they all rely on the same underlying C library, my assumption was that read speeds would be comparable between them, and factors like compression levels, chunk size, and disk I/O would deter ...
written 10 days ago by Mike Smith2.5k
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Answer: A: getBM error: The query to the BioMart webservice returned an invalid result
... Since you're in Australia, you're being redirected to the asian Ensembl mirror, which looks like it's down at the moment (https://asia.ensembl.org/index.html?redirect=no). You can force using the main Ensembl site using: mart<-useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = ...
written 12 days ago by Mike Smith2.5k
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Answer: A: Accessing a local version of BioMart (v0.9) using biomaRt
... I think the short answer here is 'No, biomaRt (the package) doesn't work with BioMart 0.9'. Exapnding on that, active development of new features for biomaRt stopped quite a number of years ago, and I can't see any obvious evidence in the code base for trying to make it compatible with BioMart 0.9. ...
written 14 days ago by Mike Smith2.5k
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Comment: C: Error with makeTxDbFromBiomart in GenomicFeatures package
... I guess this was a temporary problem, as I can run both the biomaRt query and the web interface steps without experiencing any issues.  I don't think there are geographical mirrors for the Ensembl Genomes marts, so hopefully this is working for your guys too. ...
written 15 days ago by Mike Smith2.5k
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Comment: C: Counting the number of paralogues for mouse genes gives me the wrong frequency
... I'm not sure I fully understand what the problem is.  I ran all your example code down to the # Count paralogues per gene line.  I then use dplyr to filter the results for only those containing the human PLIN4 gene I get 4 results, which seems to be what you want: > library(dplyr) > dplyr::f ...
written 19 days ago by Mike Smith2.5k
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Answer: A: biomaRT biotype TFs only
... I'm not sure biotype is quite the right field to query.  Perhaps a particular GO annotation would be appropriate.  GO:0003700 is for 'DNA binding transcription factor activity'.  It probably doesn't necessarily mean that something annotated with that is a transcription factor, but I guess it would b ...
written 21 days ago by Mike Smith2.5k
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Comment: C: where is mart hsapiens_gene_ensembl ?
... I don't know any details, only that the Ensembl team are aware of it (https://twitter.com/ensembl/status/956216658007388162) ...
written 23 days ago by Mike Smith2.5k
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Answer: A: where is mart hsapiens_gene_ensembl ?
... The main Ensembl site at www.ensembl.org seems to be unresponsive for me at the moment. You haven't provided the full code you've tried, or the output of sessionInfo() so we can see what versions of R/package you're using, but to make sure you're using one the mirror sites you need to specify the a ...
written 23 days ago by Mike Smith2.5k
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Answer: A: BiomaRT URLs down? 404 Not Found
... biomaRt updated to version 2.34.2 in the last few days, and so the version reported in your message is no longer available.  If I run the command in the same version of R I get: Installing package(s) ‘biomaRt’ trying URL 'https://bioconductor.org/packages/3.6/bioc/bin/windows/contrib/3.4/biomaRt_2 ...
written 25 days ago by Mike Smith2.5k

Latest awards to Mike Smith

Good Answer 7 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 7 months ago, created a post with more than 5 votes. For A: R: error while reading .h5 files from R using rdhf5 package
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: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 9 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 10 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 11 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Guru 11 months ago, received more than 100 upvotes.
Scholar 12 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 12 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Autobiographer 14 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 22 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 22 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 22 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Supporter 22 months ago, voted at least 25 times.
Scholar 22 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 22 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 22 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 22 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 22 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks

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