User: Mike Smith

gravatar for Mike Smith
Mike Smith2.6k
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EMBL Heidelberg / de.NBI
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http://www.msmith.de/
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3 hours ago
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8 years, 1 month ago
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Posts by Mike Smith

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Answer: A: biomaRt getBM error
... If you are in the United States then it seems that the local mirror is currently down, which may be why your query is failing (you can check by visiting http://uswest.ensembl.org) You can try to force accessing the main site by using ensembl = useMart(biomart = "ensembl", host = " ...
written 1 day ago by Mike Smith2.6k
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Answer: A: Problems Installing biomaRt
... It looks like this problem really lies with the stringi package.  It'd suggest reinstalling that as a first try, and then re-running the biomaRt installation: install.packages('stringi') It looks like that has a system dependency on ICU4C, so if you still encounter error it may be that you need ...
written 5 days ago by Mike Smith2.6k
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Comment: C: Annotation of DEXSeqHTML with biomaRt
... I don't know if it's just a copy/paste error, but the code you include for setting up biomaRt has a couple of problems.  First includeHosts> FALSE should probably be includeHosts = FALSE.  Second, the output from listMarts() can't be passed to useDataset(), you want  useMart() instead.  This shou ...
written 5 days ago by Mike Smith2.6k
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Answer: A: Difference between biomart R and biomart website GO query
... This is because when you supply a 'GO Term Accession' in the web interface, the filter it is actually applying is go_parent_term rather than just go.  This mean you also get back genes that are annotated with a child term of the GO term you've specified, where as with your biomaRt query you get back ...
written 6 days ago by Mike Smith2.6k
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Answer: A: Update from developers branch of bioconductor packages
... The planned date for the next release is 1st May.  Bioconductor works on a 6-monthly release cycle, creating a new release of all packages at these points. You can view the current timeline at http://bioconductor.org/developers/release-schedule/   ...
written 7 days ago by Mike Smith2.6k
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Comment: C: Scan error using biomart with version option
... I replied to this in https://support.bioconductor.org/p/106299/#106564 Can you make sure you're using biomaRt version 2.35.12 or newer. If that doesn't fix the issue please start a new question with a example of the code you're trying to run, plus the output of sessionInfo() so I can see what vers ...
written 4 weeks ago by Mike Smith2.6k
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Answer: A: Question about Illuminaio
... In the beadarray package we used to refer to the numeric identifier as the ProbeID, which IIRC is the Array_Address_ID in Illumina's nomenclature.  The IDs of the form ILMN_1234 were referred to as Illumina IDs in the beadarray documentation, but I guess the official manifest calls them Probe_ID. U ...
written 5 weeks ago by Mike Smith2.6k
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Comment: C: Problem retrieving data from "ENSEMBL_MART_SNP" database
... Can you provide some example data for `positionsBiomart` so I can test your code on my computer? ...
written 5 weeks ago by Mike Smith2.6k
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Comment: C: Biomart error message
... That looks correct, so maybe there's some inconsistency between you browser configuration and R. Can you try running the commands with the argument verbose = TRUE e.g. human = useMart("ensembl", dataset = "hsapiens_gene_ensembl", host = "http://Aug2017.archive.ense ...
written 6 weeks ago by Mike Smith2.6k
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Comment: C: Biomart error message
... I can run your example code fine, so I wonder if this is an issue with your internet connection. What do you see if you go to http://Aug2017.archive.ensembl.org:80/biomart/martservice?type=registry&requestid=biomaRt in your web browser? You should see some XML starting with <MartRegistry> ...
written 6 weeks ago by Mike Smith2.6k

Latest awards to Mike Smith

Good Answer 10 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 10 months ago, created a post with more than 5 votes. For A: R: error while reading .h5 files from R using rdhf5 package
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: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 12 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
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"
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
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: xcms and xcmsSet no longer works on my Mac
Guru 14 months ago, received more than 100 upvotes.
Scholar 14 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 14 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Autobiographer 17 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 24 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 24 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 24 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Supporter 24 months ago, voted at least 25 times.
Scholar 24 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 24 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 24 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 24 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 24 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks

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