User: Mark Dunning

gravatar for Mark Dunning
Mark Dunning1.0k
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Cancer Research Uk Cambridge Institute, Cambridge (until October 2017)
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@DrMarkDunning
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Senior Bioinformatics Analyst & Training co-ordinator at CRUK, Cambridge University

Bioinformatics Core Director, University of Sheffield from October 2017

Posts by Mark Dunning

<prev • 94 results • page 2 of 10 • next >
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Answer: A: How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
... I'm pretty sure that file isn't in the standard format exported by Illumina's software. Usually you expect to see columns with the prefix AVG_Signal. The following is a bit of a hack, but will give you an object to play around with;   library(limma) idata <- read.ilmn("GSE38376_non-normalized. ...
written 2.4 years ago by Mark Dunning1.0k
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Answer: A: How to normalize in R Illumina HumanHT-12 V3.0 expression beadchip data
... Not sure which text file you are referring to, but if you just want to have a look at the data and start exploring it, the easiest thing would be to load it using GEOquery. library(GEOquery) data <- getGEO("GSE38376")[[1]] ...
written 2.4 years ago by Mark Dunning1.0k
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Answer: A: Getting CDS positioning for IlluminaHumanv4 annotations
... Hi Sylvain, Not quite; the best you can do is to tell whether it is inronic, intergenic or coding   library(illuminaHumanv4.db) prbs <- mappedkeys(illuminaHumanv4CODINGZONE) table(unlist(mget(prbs, illuminaHumanv4CODINGZONE))) Intergenic Intronic Transcriptomic Transcriptomi ...
written 2.9 years ago by Mark Dunning1.0k
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Error with autoplot of transcriptDB object
... Hi all, I've having problems running some code that was previously Ok for me. Can anyone see what is going wrong? Did ggbio change how it plots transcripts? Regards, Mark >library(TxDb.Hsapiens.UCSC.hg19.knownGene) >txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene >exons <- exonsBy(txdb ...
ggbio written 3.2 years ago by Mark Dunning1.0k
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Comment: C: sampleSheet problem in beadArray
... You should probably try renaming the directory 9031292034_data to 9031292034. I don't think it will like directories with an underscore in the name. Best wishes, Mark On Thu, Aug 14, 2014 at 3:12 PM, James W. MacDonald wrote: > Hi Christine, > > The error 'Directory does not exist' ha ...
written 3.3 years ago by Mark Dunning1.0k
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plotIdeogram for non-human or mouse genome
... Hi all, I'm trying to plot an ideogram for the "dm3" genome using ggbio. I believe the following should work (it did for previous version of BioC). plotIdeogram(genome = "dm3") However, I get an error. Error in FUN("dm3"[[1L]], ...) : object 'cytobands' not found In the code I can't see where ...
ideogram ggbio written 3.3 years ago by Mark Dunning1.0k • updated 3.2 years ago by Tengfei Yin490
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Answer: A: inconsistency in illuminaHumanv4.db?
... Hi Perry, Sorry for the delay in responding. I should explain that the annotation packages that we provide are built upon the results of an in-house Perl script (described in Barbosa-Morais et al) where we map probes to the genome and transcriptome separately and collate the results. As you point o ...
written 4.0 years ago by Mark Dunning1.0k
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Comment: C: Generating GEO submission files from beadarray summary data
... I just realised that there is already a 'GEOSubmission' package on Bioconductor. Did you already try this package? Perhaps this would be a more-logical place for the conversion script to exist? Mark On Thu, Nov 14, 2013 at 9:57 PM, Kemal Akat wrote: > Hi Aliaksei, > > That would be grea ...
written 4.0 years ago by Mark Dunning1.0k
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Comment: C: SCAN.UPC for Illumina arrays?
... It would be great to have UPC support for Illumina arrays. The illuminaHumanv4 package also has the hg19 locations in it; 'illuminaHumanv4GENOMICLOCATION'. So it sounds like you have everything you need then. On Fri, Nov 15, 2013 at 6:56 PM, Steve Piccolo wrote: > Hi Tim, > > Thanks fo ...
written 4.0 years ago by Mark Dunning1.0k
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Answer: A: SCAN.UPC for Illumina arrays?
... Hi Tim, The probe sequences for illumina expression arrays are already available in the illuminaHumanV.db pacakges. e.g. illuminaHumanv4PROBESEQUENCE I'd be happy to add other fields if they would be useful for this kind of analysis. Best, Mark On Thu, Nov 14, 2013 at 10:38 PM, Tim Triche, Jr ...
written 4.0 years ago by Mark Dunning1.0k

Latest awards to Mark Dunning

Appreciated 24 months ago, created a post with more than 5 votes. For F1000 research sponsored prize for contribution to Support forum
Appreciated 2.1 years ago, created a post with more than 5 votes. For European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
Autobiographer 3.2 years ago, has more than 80 characters in the information field of the user's profile.

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