User: Raphael Gottardo

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8 years, 6 months ago
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9 years, 6 months ago
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r**************@mac.com

Posts by Raphael Gottardo

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Comment: C: PICS: vignette code outdated (use of GenomeData-object)
... We are working on this. Sent from my iPad On May 13, 2011, at 12:00 PM, Valerie Obenchain wrote: > Hi Sam, > > The error is being thrown from the .useRanges function in the setMethods.R file of the PICS package. When RangedData is coerced to GenomeData there is a call to .useRanges whic ...
written 8.5 years ago by Raphael Gottardo40
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Comment: C: ChIP-chip sequence bias not removed
... Bendikt is right, however even in the presence of a control (Input DNA or Mock-IP) a sequence based normalization will help you. Please have a look at the supplementary material of the rMAT paper where we show that on two datasets. http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/5/ ...
written 9.3 years ago by Raphael Gottardo40
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Answer: A: Reading .bpmap files for homemade tiling arrays
... Hi Larry and Patrick, Sorry for the late reply. Indeed, it is most likely the error that Larry reported. I have included a test to make sure that the groupName is valid. It should appear in the devel version, as ?of rMAT 2.5.1.? If things go well, I will push it to the Branch release next week. It' ...
written 9.5 years ago by Raphael Gottardo40
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Answer: A: Starr - MAT normalization
... Perhaps you should look at rMAT. Raphael Sent from my iPhone On May 6, 2010, at 3:29 AM, Hans-Ulrich Klein wrote: > Hi, > > the Starr vignette on page 7 says: "Besides this normalization > method, there are e.g. median rank percentile , scale, quantile, > vsn, MAT and some others ...
written 9.5 years ago by Raphael Gottardo40

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