User: Thomas J Hardcastle

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Posts by Thomas J Hardcastle

<prev • 27 results • page 1 of 3 • next >
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Answer: A: Error in frameCounting using riboSeqR
... Hi Yingying, This almost always happens because of a mismatch between the headers in the fasta file and the gene names in the bowtie file - which in turn, almost always happens because bowtie drops everything after the first space in the header file, whereas riboSeqR uses the full header. I suggest ...
written 19 months ago by Thomas J Hardcastle180
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Answer: A: Setting up Experiment Design in baySeq
... No, there's no explicit way to consider a grouping variable in a standard baySeq analysis, as the philosophy underlying the baySeq models does not really allow for this - it's not clear to me that there is any reason to expect a (log?-)linear effect on gene expression from some grouping variable. If ...
written 2.5 years ago by Thomas J Hardcastle180
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Answer: A: baySeq pairedData error
... Ok - it's the example that is out of date. If you look at section 2 of the vignette at http://bioconductor.org/packages/devel/bioc/vignettes/baySeq/inst/doc/baySeq_generic.pdf you will find the current procedure for paired data analysis, which is to construct a countData object with a three-dimensio ...
written 2.9 years ago by Thomas J Hardcastle180
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Comment: C: baySeq pairedData error
... That's odd, then. What command are you running that generates this error? ...
written 2.9 years ago by Thomas J Hardcastle180
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Answer: A: baySeq pairedData error
... You are using an old version of baySeq - please upgrade. The 'pairedData' class has been obsolete for several release cycles. Alternatively, you are using an object created with an old version of baySeq in a newer version of baySeq. The easiest way to resolve this is usually to re-run the scripts w ...
written 2.9 years ago by Thomas J Hardcastle180
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Answer: A: error in frameCounting in riboSeqR
... Sorry, the first query got lost in my inbox. frameCounting is expecting the frame of the coding sequence, relative to the first base of the RNA sequence to be contained in the GRanges object supplied. This can be calculated by taking the start of the coding sequence modulo 3; e.g. > values(gff_g ...
written 3.0 years ago by Thomas J Hardcastle180
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Answer: A: riboSeqR: legend in plotFS
... The underlying plotting function of plotFS is barplot, and you can pass barplot arguments to plotFS; the legend arguments in barplot are defined in the args.legend variable. So, if you wanted to move the legend to the top left corner: plotFS(fS, args.legend = list(x = "topleft"))   Cheers, Tom ...
written 3.9 years ago by Thomas J Hardcastle180
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Answer: A: riboSeqR: plotTranscript error
... Patched in version 1.0.5; just uploaded to Bioconductor so should emerge in a day or two. Thanks for the report. Tom --  Dr. Thomas J. Hardcastle Senior Research Associate Department of Plant Sciences University of Cambridge Downing Street Cambridge, CB2 3EA United Kingdom ...
written 4.0 years ago by Thomas J Hardcastle180
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Answer: A: riboSeqR: criteria used to determine reading frames
... A read that starts in frame with the A of the ATG will be in frame 0, that which starts in frame with the T will be in frame 1, et cetera. ...
written 4.1 years ago by Thomas J Hardcastle180
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Answer: A: riboSeqR: plotTranscript function not showing coverage
... It's actually a filled grey curve, but it will only appear if you have supplied RNA-seq data (as well as ribo-Seq) data. From your other questions, I believe that's not the case for you. Cheers, Tom ...
written 4.1 years ago by Thomas J Hardcastle180

Latest awards to Thomas J Hardcastle

Scholar 4.4 years ago, created an answer that has been accepted. For A: baySeq issues and questions

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