User: Allegra Petti

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Allegra Petti120
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Posts by Allegra Petti

<prev • 12 results • page 1 of 2 • next >
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DMR identification: minfi speed, memory problems
... Hi Kasper, I was wondering if you have any additional thoughts on the warning message below that you said "does not look nice." Any idea where it came from, how to fix it, or whether it matters? I'd really like to use bumphunter, if possible. Thanks again! Allegra _________________________________ ...
annotation convert minfi methyanalysis bumphunter written 5.5 years ago by Allegra Petti120
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Comment: C: methyAnalysis for DMR identification
... Hi Pan, Thank you very much for your helpful response. I really appreciate it! --Allegra _________________________________ Allegra A. Petti, Ph.D. The Genome Institute 4444 Forest Park Ave. St. Louis, MO 63108 apetti@genome.wustl.edu allegra.conbrio@post.harvard.edu On Feb 25, 2014, at 5:51 PM, ...
written 5.5 years ago by Allegra Petti120
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Comment: C: methyAnalysis for DMR identification
... Hi Giovanni, I got results using some arbitrarily chosen lenient parameters. I don't know yet how appropriate these parameters are for your data or mine, but in case you want to try them, I used the following command: allDMRInfo <- identifySigDMR(dmrResult, p.adjust.method="fdr", pValueTh=0.05, ...
written 5.5 years ago by Allegra Petti120
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Comment: C: methyAnalysis for DMR identification
... Hi Pan and Giovanni, I realized I have one more question. I'm currently using methyAnalysis starting from idat files, but I'd also like to be able to start from a tab-delimited matrix of beta values. I couldn't figure out how to work with (and annotate) beta values in any of the R packages that pro ...
written 5.5 years ago by Allegra Petti120
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Comment: C: methyAnalysis for DMR identification
... Hi Pan and Giovanni, Thanks for your replies, and for the advice on data visualization. I've found very little documentation for these functions, so I don't have a good feeling for the parameters and how they should be set. How is diffTh defined, and what is its range? Do lower diffTh values corres ...
written 5.5 years ago by Allegra Petti120
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Comment: C: DMR identification: minfi speed, memory problems
... data.grs seems to have the correct number of samples (56). I'm including the output of str(data.grs), but please let me know if there's anything else I should be looking at. (As I may have mentioned, I am new to R.) > str(data.grs) Formal class 'GenomicRatioSet' [package "minfi"] with 6 slots ...
written 5.5 years ago by Allegra Petti120
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Comment: C: DMR identification: minfi speed, memory problems
... Kasper, Thanks for your message and the further clarification. I will try using the additional parameters you mentioned. To answer your question, I only have 56 samples, and the size of data.grs is 237.1 Mb. I get some additional warning messages that I'm including again (below) in case they are in ...
written 5.5 years ago by Allegra Petti120
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Comment: C: DMR identification: minfi speed, memory problems
... Ah - thank you very much for the clarification!! I used 0.05 rather mindlessly because that's what the tutorial used. Best, Allegra _________________________________ Allegra A. Petti, Ph.D. The Genome Institute 4444 Forest Park Ave. St. Louis, MO 63108 apetti@genome.wustl.edu allegra.conbrio@post. ...
written 5.5 years ago by Allegra Petti120
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Comment: C: MethyLumiM to MethyLumiSet?
... Hi Tim, Thanks - this all seems extremely useful, especially the titrated mixture samples. I was thinking of generating some such (partially artificial) data sets myself, but it's great if they already exist! Allegra On Nov 6, 2013, at 6:28 PM, "Tim Triche, Jr." wrote: > Hi all, > > th ...
written 5.8 years ago by Allegra Petti120
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Comment: C: MethyLumiM to MethyLumiSet?
... Thank you very much, Tim! Sincerely, Allegra On Nov 4, 2013, at 2:19 PM, "Tim Triche, Jr." wrote: > Hi all, > > I just committed the changes to the development version of 'methylumi' and added a vignette on 450k preprocessing. The changes should propagate overnight and I will backport ...
written 5.8 years ago by Allegra Petti120

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