User: tgorri

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tgorri10
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3 years, 6 months ago
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t*****@essex.ac.uk

Creator and Maintainer of the bigmelon package. Contributor to the wateRmelon package.

Posts by tgorri

<prev • 5 results • page 1 of 1 • next >
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Answer: A: Combining pfilter (wateRmelon) and preprocessNoob (minfi)
... Hi Sara, Performing pfilter of RGChannelSets has always been problem due to how the detection p values are calculated for the probes are calculated. The previous method did return an RGChannelSet which then required the manual filtering of data after normalization but this has been changed for a wh ...
written 7 weeks ago by tgorri10
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Comment: C: Normalising GenomicMethylSet / MethylSet in Minfi
... If you have a MethylSet you will still be able to use quantile normalisation methods that are described in the wateRmelon package (I recommend dasen for general purposes). However the currently functionality of wateRmelon with minfi isn't a nice as it could be but this will be addressed in Bioconduc ...
written 2.6 years ago by tgorri10
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Comment: C: Different errors when attempting to normalize using wateRmelon (v1.1.18)
... Do you have any NAs in your rownames or colnames? I have created the error by: > data(melon) > bmel <- betas(melon) > rownames(bmel)[100] <- NA > betas(melon) <- bmel Error in (function (od, vd) : object and replacement value dimnames differ Or bmel <- betas(melon) ...
written 2.8 years ago by tgorri10
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Answer: A: Different errors when attempting to normalize using wateRmelon (v1.1.18)
... Hello Wade, This is a very interesting problem and I have not seen such an error before. I cannot seem to recreate this error using my current BioC install. And I do not think there is an issue with the code within wateRmelon as dasen has remained unchanged for a very long time (and has been workin ...
written 2.8 years ago by tgorri10
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Answer: A: Error while using BMIQ normalisation on a methylumiSet
... Hi Poojitha Thank you for your interest in the package. From what I can see this error is caused by how your methylumiset object is constructed. BMIQ by default requires the beta matrix and the probe designs (as a vector) to function correctly. In wateRmelon, we make the assumption that the probe ...
written 2.8 years ago by tgorri10

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