User: Mike Smith

gravatar for Mike Smith
Mike Smith3.9k
Reputation:
3,870
Status:
Trusted
Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
Last seen:
2 hours ago
Joined:
9 years, 5 months ago
Email:
g********@gmail.com

Posts by Mike Smith

<prev • 588 results • page 1 of 59 • next >
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Comment: A: Phyloseq to DESeq2 Help
... If you surround your table with three backticks like ` ``` ` it should format more neatly. You can also achieve this by pressing the 'code' button with 1's and 0's on it. ...
written 22 hours ago by Mike Smith3.9k
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Answer: C: biomaRt fails to retrieve GO description for some particular gene
... This occurs because a small number of the GO term descriptions contain new line characters. In the background biomaRt is basically parsing a tsv file with the results, and these new lines mess that up and you get the error you're seeing. There a fix for this in the devel branch of biomaRt e.g. `` ...
written 3 days ago by Mike Smith3.9k
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Comment: C: Can't install Genesis
... That message is saying there's a package missing that **GENESIS** requires, in this case it's **RSQLite**. R should install any dependencies during installation, but it's easily possible to get this messed up. You could try installing **RSQLite** manually using `BiocManager::install('RSQLite')`, h ...
written 9 days ago by Mike Smith3.9k
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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 9 days 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 16 days 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 20 days 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 23 days 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 28 days 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 5 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 5 weeks ago by Mike Smith3.9k

Latest awards to Mike Smith

Scholar 7 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
Teacher 7 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 7 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 7 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 7 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
Voter 7 months ago, voted more than 100 times.
Scholar 7 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 7 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Appreciated 7 months ago, created a post with more than 5 votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Scholar 7 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 7 months ago, created an answer that has been accepted. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Error: Bioconductor version '3.8' requires R version '3.5'
Teacher 7 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 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
Scholar 9 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 9 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Teacher 10 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 10 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 11 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 12 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 14 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
Teacher 15 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

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