User: Mark Dunning

gravatar for Mark Dunning
Mark Dunning50
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50
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10 years, 3 months ago
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10 years, 5 months ago
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m***********@cancer.org.uk

Posts by Mark Dunning

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Masking of limma objects by beadarray when loading arrayQualityMetrics
... Hi Marcus and others, I am now looking into this issue. I had always imagined that people with Illumina data would pre-process using beadarray and then use limma for downstream stuff such as linear modelling, therefore it would not be a problem if functions such as backgroundCorrect from limma are ...
written 10.3 years ago by Mark Dunning50
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Comment: C: Illumina Methylation. Normalization and statistics
... Hi all, Has anyone tried doing analysis on log-ratios of the red and green channels rather than beta? I would imagine they would suit existing tools such as limma and the results can always be converted back to betas afterwards. Just a thought. Mark On Thu, 2008-11-20 at 10:38 -0500, Sean Davis w ...
written 10.4 years ago by Mark Dunning50
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Answer: A: beadarray package question
... Hello, Sorry for the delay in replying. So it seems there is a bug in readIllumina when reading GEO data. In short, we assumed that there are 8 characters before the .tif extension (as happens with data produced by the Illumina scanner). However, as these files come from GEO their format is slightl ...
written 10.4 years ago by Mark Dunning50
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Answer: A: beadarray package question
... Hello, Thanks for your questions. The first relates to a new piece of functionality added to beadarray that has not been explained in depth yet. 1. The names Humanv3, Humanv2, Humanv1 etc are used to identify the type of chip being read in. This is so we know the ids of the control probes on the c ...
written 10.4 years ago by Mark Dunning50
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Comment: C: BMP4 probe '1940386' missing in illuminaHumanv2BeadID.db (as compared to illumin
... Hi all, I have taken over the building of these annotation packages and am using the same text files that Lynn linked to. In the source file, all three probe IDs (1940386, 3360703, 1850561) have "good" annotation by our criteria so I am quite puzzled by one probe is missing. My script for creatin ...
written 10.5 years ago by Mark Dunning50

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