User: Mike Smith

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Mike Smith1.5k
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EMBL Heidelberg / de.NBI
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Posts by Mike Smith

<prev • 234 results • page 1 of 24 • next >
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Answer: A: Problem with readFast5Summary in IONiseR related to HDF5
... That's an unusual error, as it means an attribute I always expect to be present in the fast5 files (essentially how long the sequencing of that read took) can't be found.  Unfortunately I can't tell from the message if that's something that affects all your files, or just one.   To begin with, I wo ...
written 1 day ago by Mike Smith1.5k
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Comment: C: How to update a package I author on Bioconductor?
... What do you mean by 'corresponding github repository'?  The primary version control for Bioconductor is their subversion server, and changes commited there are also reflected in thier github mirror.  However I don't see any recent changes to the readat package in either location. Instructions for u ...
written 2 days ago by Mike Smith1.5k
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Answer: A: Message asking to update and download from source functions when downloading pac
... This isn't strictly a Bioconductor question, but I think the important part in the output is this: There is a binary version available but the source version is later: binary source needs_compilation lattice 0.20-34 0.20-35 TRUE Do you want to install from sources the packa ...
written 3 days ago by Mike Smith1.5k
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Answer: A: Problem with the readFast5Summary command
... I've tested the package with your files and it seems to work fine.  I suspect the error you're seeing is because the file can't be accessed.  You need to make sure the path to the files is either absolute i.e. starting at the root of your system, or is relative to the current working directory of yo ...
written 10 days ago by Mike Smith1.5k
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Comment: C: Problem with the readFast5Summary command
... Hi, Thanks for providing the example files.  I'm on holiday at the moment, but I'll take a look at this error when I get back next week.  It's not something I've seen before, so maybe the file format has changed again. Cheers, Mike ...
written 14 days ago by Mike Smith1.5k
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Answer: A: Q score filter to each base in QualityScaledDNAStringSet
... You can do something like this.  First we'll create an example QualityScaledDNAStringSet using the example in the help page library(Biostrings) x1 <- DNAStringSet(c("TTGA", "CTCN")) q1 <- PhredQuality(c("*+,-", "6789")) qx1 <- QualityScaledDNAStringSet(x1, q1) Then we'll create a list co ...
written 20 days ago by Mike Smith1.5k
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Comment: C: Installation of Bioconductor package: lpsymphony
... If you're still trying to get hold of the complete output from the installation, you can try using the linux script command.  In a terminal you'd do something like: $ script /my/logfile.txt $ R > BiocInstaller::biocLite("lpsymphony") ....... > q() $ exit Everything that was printed to scree ...
written 20 days ago by Mike Smith1.5k
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Comment: C: Installation of Bioconductor package: lpsymphony
... Maybe I'm missing something, but isn't the point of lpsymphony to remove the need to have SYMPHONY already installed on the system.  From the package's DESCRIPTION file: The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while R ...
written 22 days ago by Mike Smith1.5k
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Answer: A: IONiseR readFast5Summary Error
... Thank you for providing the files.  These currently haven't been based-called, the only data in there is the raw-signal.  You're using an older version of R and IONiseR (R is now on version 3.3.2), and at the time the version you're using was written it wasn't possible to produce fast5 files like th ...
written 22 days ago by Mike Smith1.5k
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Comment: C: IONiseR readFast5Summary Error
... Does it do this is you try only a single file? e.g. fast5files <- list.files(path = "/home/ferrato/Documents/fast5", pattern = ".fast5$",full.names = TRUE) example.summary <- readFast5Summary(fast5files[1]) If it does, can you make that one file available to me, so I can try and debug the c ...
written 22 days ago by Mike Smith1.5k

Latest awards to Mike Smith

Scholar 23 days ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Guru 4 weeks ago, received more than 100 upvotes.
Scholar 5 weeks ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
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Teacher 11 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 11 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 11 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 11 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 11 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 11 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Scholar 11 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 11 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 11 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: Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more g
Scholar 12 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Scholar 13 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 13 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
Scholar 13 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
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Scholar 13 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
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