User: Mike Smith

gravatar for Mike Smith
Mike Smith1.7k
Reputation:
1,740
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Location:
EMBL Heidelberg / de.NBI
Website:
http://www.msmith.de/
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4 hours ago
Joined:
7 years, 3 months ago
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g********@gmail.com

Posts by Mike Smith

<prev • 268 results • page 1 of 27 • next >
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Comment: C: R: error while reading .h5 files from R using rdhf5 package
... Can you update your post to include the output from the command sessionInfo() so we can see what version of R and rhdf5 you are using?  It seems to work fine for me e.g. library(rhdf5) ##create temp file location and download to there file_loc <- file.path(tempdir(), "h5ex_d_sofloat.h5") downlo ...
written 13 hours ago by Mike Smith1.7k
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Answer: A: Problem in extracting a row from matrix in rhdf5
... This should be fixed in rhdf5 version 2.21.2.  I use H5DOpen() to access the dataset, but hopefully this example is demonstrates the fix. library(rhdf5) tf <- tempfile(fileext = ".h5") download.file(url = "http://msmith.de/data/h5tutr_dset.h5", destfile = tf, quiet ...
written 9 days ago by Mike Smith1.7k
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Comment: C: biomaRt - Error in getBM: The query to the BioMart webservice returned an invali
... I'm using the developmental version found here (https://bioconductor.org/packages/devel/bioc/html/biomaRt.html) but at the moment I can't reproduce your error with 2.32.0 either.  It works fine for me running that query against all four of the Ensembl mirrors.  If it is still failing for you can you ...
written 15 days ago by Mike Smith1.7k
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Answer: A: biomaRt - Error in getBM: The query to the BioMart webservice returned an invali
... I suspect this problem was related to the update to Ensembl 89 (i.e. https://support.bioconductor.org/p/96585/) and you were unfortunate to query during the transition time.  For me the code seems to work fine now e.g. getBM(attributes= c('ensembl_gene_id','entrezgene','hgnc_id','hgnc_symbol'), ...
written 16 days ago by Mike Smith1.7k
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Comment: C: Problem in extracting a row from matrix in rhdf5
... Hi Filipe, Thanks for reporting this.  I've managed to reproduce this with a simple example.  I'll look into why it's happening and report back once I've got a solution. ...
written 5 weeks ago by Mike Smith1.7k
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Answer: A: topGO gene names/ensembl IDs
... I'm afraid I can't help with the topGO part, but to retain the mapping between your query and the returned values with biomaRt, you can normally list the same variable as both an attribute and a filter.   At the moment it looks like you aren't specifying what variable you want to filter on, so the ...
written 6 weeks ago by Mike Smith1.7k
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Answer: A: BiomaRt xenopus tropicalis genome unavailable
... Hi Anne, I'm afraid biomaRt (the package) doesn't really work like that.  It is designed to provide a way to connect to data stores that are running BioMart (the service) as a way to query their databases.  Ensembl is by far the most widely used of these data stores, but there are many other smalle ...
written 6 weeks ago by Mike Smith1.7k
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Comment: C: Error with read.idat() function in illuminaio package
... Normally it's a good idea to ask a new question here, rather than adding an 'answer' to an existing one.  People are more likely to notice a new question with no answers, than bumping something old. Looking at this, the data are unusual, but it's basically the same problem as was identified before ...
written 7 weeks ago by Mike Smith1.7k
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Comment: C: Inconsistencies in biomart results
... No problem, this seemed like a bit of an insidious bug when I thought about it.   Let me know if it causes any issues your end.  I don't know if you ever ban IPs or anything, but if someone asks for data on 30,000 genes you'll get 60 queries in quick succession now, which might look strange in the ...
written 7 weeks ago by Mike Smith1.7k
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Answer: A: Inconsistencies in biomart results
... Dredging up an old post here, but I've modified the getBM() function in biomaRt to submit queries in batches if the number of values exceeds 500.  If you have multiple filters each of which have more than 500 values it should generate multiple mutually exclusive queries so that all combinations are ...
written 7 weeks ago by Mike Smith1.7k

Latest awards to Mike Smith

Scholar 8 weeks ago, created an answer that has been accepted. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: biomaRT GO-ID retreival showing different genes than AmiGO
Scholar 10 weeks ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Scholar 3 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Guru 3 months ago, received more than 100 upvotes.
Scholar 4 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Scholar 4 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Autobiographer 6 months ago, has more than 80 characters in the information field of the user's profile.
Scholar 14 months ago, created an answer that has been accepted. For A: arrayQualityMetrics error: Error: Unknown parameters: cex.axis
Teacher 14 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 14 months ago, created an answer with at least 3 up-votes. For A: DESeq2 color coding
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: xcms and xcmsSet no longer works on my Mac
Supporter 14 months ago, voted at least 25 times.
Scholar 14 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 14 months ago, created an answer that has been accepted. For A: DESeq2 color coding
Scholar 14 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website
Scholar 14 months ago, created an answer that has been accepted. For A: Retrieve SNP flanking sequences in biomaRt
Scholar 14 months ago, created an answer that has been accepted. For A: Install problems on centos 7 of TCGAbiolinks
Scholar 14 months ago, created an answer that has been accepted. For A: Any quick solution for fixing error : "$ operator is invalid for atomic vectors"
Teacher 14 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 14 months ago, created an answer that has been accepted. For A: Intergenic coordinates with Genomic Feaures
Scholar 15 months ago, created an answer that has been accepted. For A: ENCODExplorer doesn't return results which are on the website

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