User: Mike Smith

gravatar for Mike Smith
Mike Smith3.9k
Reputation:
3,900
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Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
8 hours ago
Joined:
9 years, 6 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 595 results • page 2 of 60 • next >
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Answer: A: Can't install Genesis
... There doesn't seem to be any errors here, the installation of GENESIS looks like it worked fine. If you're worried by the part that says: > installation path not writeable, unable to update packages: boot, cluster, foreign, nlme this is likely because R was installed using administrator pri ...
written 4 weeks ago by Mike Smith3.9k
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Answer: A: Eliminate redundancy in biomaRt (2.38.0) query
... The `getBM()` function has the argument `uniqueRows` which toggles this behaviour. However the default value is `TRUE` so it should do this unless explicitly asked not to. Do you have an example query where it isn't working correctly? ...
written 5 weeks ago by Mike Smith3.9k
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Comment: C: windows tximport fail
... Your call to `rhdf5::h5read()` needs to you to specify the name of the dataset to extract via the `name` argument. That's the source of the error your getting there. To try and recreate the tximport usage you want to try `rhdf5::h5ls()` which will grab the entire contents of the file. ...
written 6 weeks ago by Mike Smith3.9k
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Comment: C: Dealing With Package Sizes Greater than 5 MB
... You might get a better response posting this to the Bioc Developers mailing list, which is more focused on issues like this. You can sign up at https://stat.ethz.ch/mailman/listinfo/bioc-devel There was a post very recently on this same topic which may be useful: https://stat.ethz.ch/pipermail/bioc ...
written 6 weeks ago by Mike Smith3.9k
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Answer: A: error pushing to git/bioconductor
... Your upstream remote is for the **BiocGenerics** package, rather than **AnalysisPageServer**. Perhaps try: ``` git remote rm upstream git remote add upstream git@git.bioconductor.org:packages/AnalysisPageServer.git ``` --- Also note that you might get a faster response to queries like this on th ...
written 7 weeks ago by Mike Smith3.9k
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Answer: A: System dependent biomaRt curl ssl error "wrong version number"
... This should now be fixed in biomaRt version 2.40.3. It will take a few days to propagate through to the Bioconductor repository. ``` > library(biomaRt) > Biobase::package.version("biomaRt") [1] "2.40.3" > species <- "hsapiens_gene_ensembl" > ensemblversion <- "97" > ensmart & ...
written 8 weeks ago by Mike Smith3.9k
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Comment: C: System dependent biomaRt curl ssl error "wrong version number"
... Can you provide the output of `sessionInfo()` so we can see which version of biomaRt you are using? There's definitely something odd going on as it's specify `https` and port 80 which is probably incompatible, and will be due to a bug in trying to match up the 'current version' URL with the fact th ...
written 9 weeks ago by Mike Smith3.9k
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Comment: C: how to run old scripts using corresponding biomaRt versions from archives
... I think I need to spend some time clarifying / updating the `useEnsembl()` function because it's primarily focused on the main Ensembl site, rather than EnsemblGenomes - that's understandably not clear from the function name! The only archive that I know of for Ensembl Plants is from October 2017 ( ...
written 9 weeks ago by Mike Smith3.9k
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Comment: C: external_gene_id attribute removed from new biomaRt version
... Ensembl Plants has fewer archives than the main Ensembl site (I only know of http://oct2017-plants.ensembl.org ) so it's harder to check if things have changed, but I don't see an `external_gene_id` there either: ``` > ensembl <- useMart(biomart = "plants_mart", + dataset ...
written 9 weeks ago by Mike Smith3.9k
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Comment: C: external_gene_id attribute removed from new biomaRt version
... Which dataset are you trying to use? I'm not sure there has ever been an `external_gene_id` attribute for *hsapiens* (at least not looking at archives back for the past few years), do you mean to use `external_gene_name`? You can search for the available attributes with `searchAttributes()` e.g to ...
written 9 weeks ago by Mike Smith3.9k

Latest awards to Mike Smith

Scholar 4 weeks ago, created an answer that has been accepted. For A: 'biomaRt expected a character string of length 1' error with getBM and reseq mrn
Scholar 8 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: getBM error: The query to the BioMart webservice returned an invalid result
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: 'biomaRt expected a character string of length 1' error with getBM and reseq mrn
Scholar 8 months ago, created an answer that has been accepted. For A: 'biomaRt expected a character string of length 1' error with getBM and reseq mrn
Scholar 8 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Voter 8 months ago, voted more than 100 times.
Scholar 8 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 8 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 8 months ago, created an answer that has been accepted. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Scholar 8 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: getBM error: The query to the BioMart webservice returned an invalid result
Appreciated 8 months ago, created a post with more than 5 votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 9 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: getBM error: The query to the BioMart webservice returned an invalid result
Scholar 10 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 10 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Is there a way to tell biocLite() to install a Bioconductor package only if it i
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 12 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 13 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 15 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 16 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages

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