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User: Mike Smith

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Mike Smith3.2k
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3,250
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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32 minutes ago
Joined:
8 years, 11 months ago
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Posts by Mike Smith

<prev • 504 results • page 1 of 51 • next >
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Answer: A: biomart not ound some prevous release
... **biomaRt** lists the Ensembl archives found at http://www.ensembl.org/info/website/archives/index.html If the version that you want is not found there, then it has probably been permanently retired by Ensembl. You can try to contact them to see if you can obtain an offline version of the annotatio ...
written 2 days ago by Mike Smith3.2k
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Answer: A: indexBam(), summarizeOverlaps() error: RNA-seq
... I think there's a few different issues here. I've download the testis bam and you code ran without errors, so it's not not an inherent issue with your code or the tools. Give this, I would verify that the bam files you've obtained have downloaded correctly. The `EOF marker is absent` error certa ...
written 2 days ago by Mike Smith3.2k
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Answer: A: How to fix 'long vectors not supported yet' error in R
... The error message you are seeing is because you're iterating the for-loop over every entry in a vector that is longer than 2^31-1. You can verify that's where the message comes from with the following example: ``` for(i in 1:(2^44)) { print(i) } Error in for (i in 1:(2^44)) { : long vector ...
written 2 days ago by Mike Smith3.2k
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Answer: C: Error in DESeq2 installation with linux env.: non zero exit status (and RcppArma
... The first thing to note is that this isn't a problem with **DESeq2**. The message `ERROR: dependency ‘RcppArmadillo’ is not available for package ‘DESeq2’` tells you that the reason **DESeq2** isn't being installed is because **RcppArmadillo** isn't available. So you really want to focus on sortin ...
written 7 days ago by Mike Smith3.2k
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Comment: C: CMD check warning using Bioconductor as a source for the dependencies of an R pa
... You can find further details in [https://win-builder.r-project.org/incoming_pretest/Miso_0.2.0_20190210_133229/Windows//00install.out][1] I wonder if this is because the Windows builder is stuck with an outdated version of a Bioconductor package that still references **BiocInstaller**. Perhaps the ...
written 9 days ago by Mike Smith3.2k
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Answer: C: Issue with TCGAbiolinks package.
... It looks like this was a bug that was fixed a few weeks ago (https://github.com/BioinformaticsFMRP/TCGAbiolinks/commit/8c5449958ad2e1cd300daa033d57d1267e7c9d6d) I would do a `BiocManager::install('TCGAbiolinks')` to get version 2.10.3 and try from there. ...
written 13 days ago by Mike Smith3.2k
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Comment: C: Issue with TCGAbiolinks package.
... Can you update your post to include the output of `sessionInfo()` so we can see which versions of R and TCGAbiolinks you're using. I get errors earlier in your example code with my setup: ``` > library(TCGAbiolinks) > Tumor <- c("BLCA") > query <- GDCquery(project = paste("TCGA-",Tu ...
written 13 days ago by Mike Smith3.2k
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Comment: C: Cannot install DESeq2
... You'll need to show us the output from `install.packages('RcppArmadillo')`, otherwise it's impossible to diagnose what has failed. ...
written 15 days ago by Mike Smith3.2k
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Answer: A: Cannot install DESeq2
... You need to install the xml2 system library. If you're running Ubuntu you can do this by entering the following in a command line terminal: ``` sudo apt-get install libxml2-dev ``` and for Redhat / CentOS it's something like: ``` sudo yum install libxml2-devel. ``` Since this is a system librar ...
written 15 days ago by Mike Smith3.2k
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Comment: C: Arrayquality metrics Warning - Warning message in maximumLevels(fac, n = length(
... Taking a closer look, this is coming from the `aqm.heatmap` function where a single colour palette is passed to `maximumLevels` , so this does happen with the current version. I guess it's not common to encounter more than 9 level in a single covariate, so this doesn't crop up much. ...
written 19 days ago by Mike Smith3.2k

Latest awards to Mike Smith

Teacher 11 weeks 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 11 weeks ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 3 months ago, created an answer that has been accepted. For A: How to combine sequences from different stringsets?
Scholar 3 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Teacher 4 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 4 months ago, created an answer with at least 3 up-votes. For A: BioParallel::BatchtoolsParam() - how to pass customized resource variables to ba
Scholar 5 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 6 months ago, created an answer that has been accepted. For A: Update from developers branch of bioconductor packages
Scholar 8 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: Update from developers branch of bioconductor packages
Teacher 9 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
Scholar 20 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 20 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 20 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
Scholar 20 months ago, created an answer that has been accepted. For A: BiomaRT URLs down? 404 Not Found
Scholar 20 months ago, created an answer that has been accepted. For A: biomaRt error in useMart
Scholar 20 months ago, created an answer that has been accepted. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 20 months ago, created an answer that has been accepted. For A: biomaRt is not working
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Please use the function 'listAttributes' to get valid attribute names
Scholar 20 months ago, created an answer that has been accepted. For A: biomaRt scan error for latest assembly when indicating version Number
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: HDF5 reading speed
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Scan error using biomart with version option
Scholar 20 months ago, created an answer that has been accepted. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: biomaRt: drerio_gene_ensembl dataset missing
Scholar 20 months ago, created an answer that has been accepted. For A: Please use the function 'listAttributes' to get valid attribute names

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