User: Mike Smith

gravatar for Mike Smith
Mike Smith2.0k
Reputation:
2,000
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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22 minutes ago
Joined:
7 years, 6 months ago
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g********@gmail.com

Posts by Mike Smith

<prev • 310 results • page 1 of 31 • next >
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Answer: A: org.Mm.eg.db UNIPROT missing values
... If you take a look at the manual pages for org.Mm.eg.db it gives the following details on how the Uniprot mappings are derived:  "This object is a simple mapping of Entrez Gene identifiers https://www.ncbi.nlm.nih.gov/ entrez/query.fcgi?db=gene to Uniprot Accession Numbers" So we can take a look a ...
written 5 days ago by Mike Smith2.0k
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Answer: A: DESeq2 had non-zero exit status
... I don't think this is an issue with DESeq2 per se, but more likely that some of those packages you are unable to install are missing system libraries, and when those packages fail installation DESeq2 fails too.   My advice would be too try installing each of the failing packages seperately, and loo ...
written 5 days ago by Mike Smith2.0k
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Comment: C: Problem with readFast5Summary in IONiseR related to HDF5
... It looks like EventDetection data is not available in the file you provided.  IONiseR assumed this would always be present, and didn't have any checks built in to make sure this was true.  I've patched it so the example file you can be read.  This is available in IONiseR version 2.1.1.  That should ...
written 5 days ago by Mike Smith2.0k
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Comment: C: makeTxDbFromBiomart error while building metadata dataframe
... This seems to work for me. makeTxDbFromBiomart(biomart="ensembl", dataset="mmusculus_gene_ensembl", transcript_ids=NULL, circ_seqs=DEFAULT_CIRC_SEQS, filter=NULL, id_prefix="ensembl_", host="www.ensembl.org", port=80, ...
written 5 days ago by Mike Smith2.0k
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Answer: A: Errors with makeTxDbFromBiomart
... It doesn't look like makeTxDbFromBiomart() copes very well if you use a host that isn't www.ensembl.org.  It goes off and tries to find the metadata on an specific ftp site, and that fails when you're asking for a fungal genome.  Perhaps it's most straightforward to use makeTxDbFromGFF() instead.  Y ...
written 5 days ago by Mike Smith2.0k
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Comment: C: Get cytoband from refsnp ID using biomaRt in R
... Glad it works for you.  I've updated my post to fix the typo, this shows why you should clear your environment before testing a solution! Can you give an rsID example that produces the CHR annotations?  I guess that doesn't show up with my 3 examples, so I'm just curious to know where they're comin ...
written 10 days ago by Mike Smith2.0k
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Comment: C: hyperlink issue with a R package
... Ok, so you're really close in your example, but the issue is with the class of data you're giving to the x argument.  To understand this a bit better, lets look at your gsub() outside of the function call: genes <- gsub("DoseResponse_Curves/drCurve_", "", gsub(".pdf", "", plotPaths)) is(genes) ...
written 10 days ago by Mike Smith2.0k
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Comment: C: hyperlink issue with a R package
... I have tried it and can get it to work fine. Why don't you include your complete code here, from reading the file to writing it back out, like in my first example, and we'll see if we can find the issue. ...
written 11 days ago by Mike Smith2.0k
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Comment: C: hyperlink issue with a R package
... Ok, that's good progress.  If you check the comment right at the bottom of the page in that vignette it says "to change the display text for a hyperlink column just write over those cells".  That implies to me that we need to write the values in this column twice; first to put in the hyperlink, seco ...
written 11 days ago by Mike Smith2.0k
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Comment: C: hyperlink issue with a R package
... I'm very much in favour of trying to encourage people to try and solve problems themselves, and I don't think the 8 minutes between our two posts is indicative of much effort.  I will point out that the tab object created in the code above contains everything in the Excel file, including a column w ...
written 12 days ago by Mike Smith2.0k

Latest awards to Mike Smith

Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: R: error while reading .h5 files from R using rdhf5 package
Appreciated 3 months ago, created a post with more than 5 votes. For A: R: error while reading .h5 files from R using rdhf5 package
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 3 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 5 months ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 5 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 6 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Guru 6 months ago, received more than 100 upvotes.
Scholar 7 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 7 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Autobiographer 9 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 17 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Teacher 17 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 17 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Supporter 17 months ago, voted at least 25 times.
Scholar 17 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 17 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Scholar 17 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 17 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 17 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks

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