User: Mark Dunning

gravatar for Mark Dunning
Mark Dunning1.1k
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Location:
Sheffield, Uk
Website:
http://sbc.shef.ac.uk/
Twitter:
@DrMarkDunning
Last seen:
2 months, 3 weeks ago
Joined:
10 years, 6 months ago
Email:
m***********@gmail.com

Bioinformatics Core Director, The University of Sheffield

Posts by Mark Dunning

<prev • 101 results • page 2 of 11 • next >
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Answer: A: Normalization of Illumina Microarray Data
... The "raw data" for this dataset seem to be the annotation files for the arrays, and not the raw intensities at all. So not helpful for analysis. However, you can use the GEOquery package to import the normalised intensities library(GEOquery) remotefile <- "ftp://ftp.ncbi.nlm.nih.gov/geo/series ...
written 2.5 years ago by Mark Dunning1.1k
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News: Course: Analysis of RNA-seq and ChIP-seq data, March 29th - April 1st, Oeiras, Portugal
... Hi all, Registration is open for a four-day workshop on the analysis of RNA- and ChIP-seq data in Bioconductor in the pleasant surroundings of Oeiras (nr Lisbon) Portugal. We will be covering the basics of NGS analysis in Bioconductor, quality assessment of NGS data and workflows for RNA-seq and Ch ...
news workshop course written 3.6 years ago by Mark Dunning1.1k
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News: F1000 research sponsored prize for contribution to Support forum
... Hi all, Just to let you know that during the European Bioconductor Developers meeting next week, a prize will be awarded to the individual with greatest contribution to this support forum. The prize is being sponsored by F1000 research, who as you probably know recently launched a dedicated Biocon ...
news written 3.8 years ago by Mark Dunning1.1k
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Comment: C: biomaRt package problem
... Ooops. Sorry didn't see that. Thanks Mark ...
written 3.8 years ago by Mark Dunning1.1k
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Comment: C: biomaRt package problem
... Any news on this yet? I'm getting the same problem :/ ...
written 3.8 years ago by Mark Dunning1.1k
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Answer: A: European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
... Hi Phil, Sorry, it will be an 09:30 start on the Monday. This is so that we can finish early on the Tuesday to allow people to catch flights back etc. The timetable will be announced very shortly along with a list of invited speakers. Best wishes, Mark ...
written 4.0 years ago by Mark Dunning1.1k
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News: European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
... Hi all, We are pleased to announce that that European Bioconductor Developers Conference will take place in Cambridge, England from 7th-8th December 2015. The meeting is aimed at bioinformaticians, programmers and software engineers who contribute to the Bioconductor project, or are interested in ...
news workshop developers conference written 4.0 years ago by Mark Dunning1.1k • updated 3.9 years ago by Laurent Gatto1.2k
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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 4.2 years ago by Mark Dunning1.1k
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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 4.2 years ago by Mark Dunning1.1k
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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 4.8 years ago by Mark Dunning1.1k

Latest awards to Mark Dunning

Centurion 19 months ago, created 100 posts.
Popular Question 19 months ago, created a question with more than 1,000 views. For European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
Popular Question 19 months ago, created a question with more than 1,000 views. For plotIdeogram for non-human or mouse genome
Popular Question 19 months ago, created a question with more than 1,000 views. For ggsave option for ggbio Tracks function
Popular Question 19 months ago, created a question with more than 1,000 views. For plotIdeogram for non-human or mouse genome
Popular Question 2.3 years ago, created a question with more than 1,000 views. For European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
Appreciated 2.3 years ago, created a post with more than 5 votes. For F1000 research sponsored prize for contribution to Support forum
Appreciated 3.8 years ago, created a post with more than 5 votes. For F1000 research sponsored prize for contribution to Support forum
Appreciated 4.0 years ago, created a post with more than 5 votes. For European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
Autobiographer 5.0 years ago, has more than 80 characters in the information field of the user's profile.

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