User: Mike Smith

gravatar for Mike Smith
Mike Smith510
Reputation:
510
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
20 minutes ago
Joined:
5 years, 11 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 40 results • page 1 of 4 • next >
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Answer: A: R ShortRead : Merge list of ShortReadQ object
... You can try using the `append()` method on the list e.g. ## List of two ShortReadQ objects with different widths > fq [[1]] class: ShortReadQ length: 256 reads; width: 36 cycles [[2]] class: ShortReadQ length: 256 reads; width: 30 cycles ## Combine to a sin ...
written 14 days ago by Mike Smith510
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Comment: C: 98.21% of input gene IDs are fail to map
... Yes look like it is. ...
written 19 days ago by Mike Smith510
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Answer: A: 98.21% of input gene IDs are fail to map
... The root of your problem is that your gene names are all upper case, but for rat (and mouse etc) generally only the first letter is capitalised, and the `bitr` conversion is case sensitive. We can use the function `str_to_title` in the **stringr** package to fix this: install.packages('stringr ...
written 19 days ago by Mike Smith510
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Answer: C: How can I uninstall my packages in Rstudio
... Remove a package with `remove.packages()` e.g. remove.packages("affycoretools") **Affycoretools** is a Bioconductor pacakge, so reinstallation needs their install script / the **BiocInstaller** package e.g. source("https://bioconductor.org/biocLite.R") biocLite("affycoretools") ...
written 22 days ago by Mike Smith510
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Comment: C: Error in BioMartVersion
... Can you update your post to include the output of `sessionInfo()` so we can see which versions of **R** and **biomaRt** you're using? I suspect your package is a little out of data, www.biomart.org hasn't been the relevant website to check for quite a while & that error message is no longer in ...
written 22 days ago by Mike Smith510
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Answer: A: Error using BioMart. No encoding supplied.
... For me the Ensembl mirror sites are down.  It looks like you're US based, so by default you'll get redirected to [uswest.ensembl.org](http://uswest.ensembl.org/biomart/martview?redirect=no) or [useast.ensembl.org](http://useast.ensembl.org/biomart/martview?redirect=no), neither of which are working ...
written 4 weeks ago by Mike Smith510
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Comment: C: biomaRt mmusculus_gene_ensembl dataset
... I'm afraid I don't know enough about the BioMart internals to answer that, I just work with the API. It definitely added confusion to this issue though. ...
written 9 weeks ago by Mike Smith510
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Comment: C: biomaRt mmusculus_gene_ensembl dataset
... `listDatasets()` just grabs it's information from [http://www.ensembl.org/biomart/martservice?type=datasets&mart=ENSEMBL_MART_ENSEMBL][1] (or the equivalent for other marts). If you refresh that page you'll get the list in different orders. Hence the entries containing the apostrophes appeare ...
written 9 weeks ago by Mike Smith510
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Answer: A: biomaRt mmusculus_gene_ensembl dataset
... This issue was caused by the introduction of the new primate species, which include apostrophes in their description fields (e.g. *aotus nancymaae* (Nancy Ma's night monkey) ), and **biomaRt** was unable to process these correctly. This has now been patched, and if you update your version of **biom ...
written 9 weeks ago by Mike Smith510
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Answer: A: biomaRt: Cannot access the zebra fish dataset
... There was an issue with one of the new primate datasets having an apostrophe in its description, which was causing `listDatasets()` to fail. I have patched this in version 2.35.1 and pushed it to the Bioconductor devel branch. This will take a few days to propagate, so the fastest way to get hold if ...
written 10 weeks ago by Mike Smith510

Latest awards to Mike Smith

Scholar 19 days ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 22 days ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 4 weeks ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 9 weeks ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 5 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio
Scholar 9 months ago, created an answer that has been accepted. For A: Retrieve all genes under a mammalian phenotype ontology term
Autobiographer 10 months ago, has more than 80 characters in the information field of the user's profile.
Appreciated 4.0 years ago, created a post with more than 5 votes. For A: Using Illumina Ht-12 Without Genomestudio
Teacher 4.0 years ago, created an answer with at least 3 up-votes. For A: Using Illumina Ht-12 Without Genomestudio

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