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:
1 month ago
Joined:
10 years, 9 months ago
Email:
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Bioinformatics Core Director, The University of Sheffield

Posts by Mark Dunning

<prev • 102 results • page 1 of 11 • next >
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Answer: A: How to convert dataframe into ExpressionSetIllumina / summarized data with beada
... I would probably start by reading these data using `limma` ```data <- limma::read.ilmn("GSE22247_non-normalized_data.txt",expr = "SAMPLE") ``` and then following steps from the limma user guide for normalisation ...
written 4 weeks ago by Mark Dunning1.1k
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Comment: C: Obtaining annotated results from rnbeads
... Thanks a lot. That does indeed work. ...
written 6 months ago by Mark Dunning1.1k
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Comment: C: Obtaining annotated results from rnbeads
... Thanks a lot. That does indeed work. ...
written 6 months ago by Mark Dunning1.1k
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Obtaining annotated results from rnbeads
... I'm trying to use `rnbeads` to analyse some EPIC methylation arrays. I'm calling the functions individually, rather than running the single report script, so that I have more control over the differential analysis. I use this code to perform differential methylation and export tables ``` rnb.set ...
rnbeads epic written 6 months ago by Mark Dunning1.1k • updated 6 months ago by mscherer10
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Comment: C: Annotation of probes from Affymetrix and Illumina platforms in MACQ project ?
... The `illuminaHumanv1.db` package has mappings between this Illumina chip and Symbol, entrez, etc. The keytype you need to use is `PROBEID` library(illuminaHumanv1.db) anno <- select(illuminaHumanv1.db, keytype="PROBEID",keys=ENTREZID,columns=c("ENTREZID","SYMBOL")) head(anno) ...
written 7 months ago by Mark Dunning1.1k
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Error: C stack usage when installing Txdb package
... Hi all, I'm trying to install the TxDb.Hsapiens.UCSC.hg38.knownGene package, but getting pretty stumped at an error to do with C stack usage.   source("http://www.bioconductor.org/biocLite.R") biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene")   BioC_mirror: https://bioconductor.org Using Biocon ...
org.hs.eg.db txdb.hsapiens.ucsc.hg38.knowngene written 24 months ago by Mark Dunning1.1k • updated 24 months ago by Simon Anders3.6k
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Job: Sheffield Bioinformatics Core Analyst
... The Bioinformatics Core at The University of Sheffield is looking for an Analyst with strong statistical skills and awareness of best-practices and reproducible research. Please see below for a summary and how to apply Summary The University of Sheffield and its associated Medical School and Hospi ...
job bioinformatician job bioinformatics core written 2.0 years ago by Mark Dunning1.1k
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Comment: C: Probe summerization of Human HT-12 V4 BeadChip arrays
... What version of Bioconductor are you using? It seems fine for me on Bioconductor 3.6.   library(GEOquery) gse <- getGEO("GSE33126")[[1]] eset <- as(gse, "ExpressionSetIllumina") sessionInfo() I wouldn't recommend averaging the probes for the same gene though. Some of the probes on these ar ...
written 2.0 years ago by Mark Dunning1.1k
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Job: Sheffield Bioinformatics Core Analyst
... The Bioinformatics Core at The University of Sheffield is looking for an Analyst. If best-practice Bioinformatics and reproducible research is your thing, check-out the full details below:- http://www.jobs.ac.uk/job/BDQ610/sheffield-bioinformatics-core-analyst/   ...
job data analyst bioinformatics core written 2.3 years ago by Mark Dunning1.1k
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Job: Sheffield Bioinformatics Core Analyst
... The Bioinformatics Core at The University of Sheffield is looking for an Analyst. If best-practice Bioinformatics and reproducible research is your thing, check-out the full details below:- http://www.jobs.ac.uk/job/BBM484/sheffield-bioinformatics-core-analyst/ ...
job data analyst uk bioinformatics core written 2.5 years ago by Mark Dunning1.1k

Latest awards to Mark Dunning

Centurion 21 months ago, created 100 posts.
Popular Question 21 months ago, created a question with more than 1,000 views. For European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
Popular Question 21 months ago, created a question with more than 1,000 views. For plotIdeogram for non-human or mouse genome
Popular Question 21 months ago, created a question with more than 1,000 views. For ggsave option for ggbio Tracks function
Popular Question 21 months ago, created a question with more than 1,000 views. For plotIdeogram for non-human or mouse genome
Popular Question 2.5 years ago, created a question with more than 1,000 views. For European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
Appreciated 2.5 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 F1000 research sponsored prize for contribution to Support forum
Appreciated 4.2 years ago, created a post with more than 5 votes. For European Bioconductor Developers Meeting: Cambridge 7/8th December 2015
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.

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