User: Pan Du

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Pan Du440
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Posts by Pan Du

<prev • 44 results • page 1 of 5 • next >
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Answer: A: error on detecting regions
... Hi Please update your R and methyAnalysis package to the latest released versions (R 3.1.0, methyAnalysis 1.6.0), and send me the error messages and related data if it still happens. Thanks! Pan On Tue, Jun 17, 2014 at 2:30 PM, guest [guest] wrote: > Dear Users, > > I met an error th ...
written 4.3 years ago by Pan Du440
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Answer: A: how to set up sampleInfo for methylation array in illumina 450K
... Hi I guess you didn't input the sampleInfo correctly. Based on your filename "sampleInfo_12.csv", it is a csv file, not a Tab delimited file. So try to import the file using read.csv function. I also noticed there are "SENTRIX_ID" columns together with "SENTRIX_BARCODE" and "SENTRIX_POSITION". The ...
written 4.5 years ago by Pan Du440
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Comment: C: methyAnalysis for DMR identification
... Hi Allegra In order to get the MethyLumiM object, you must have the methylated and unmethylated probe intensities in your tab-delimited files. The beta- values were basically calculated from the methylated and unmethylated probe intensities. I recommend using .IDAT files if you have them because it ...
written 4.6 years ago by Pan Du440
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Comment: C: methyAnalysis for DMR identification
... Hi Allegra and Giovanni The parameters of identifySigDMR need to be tuned based on your dataset. The default parameters was designed for the cell lines with clear difference between groups. For tissue samples, these parameters need to be less stringent, especially the diffTh parameter. Also, I stro ...
written 4.6 years ago by Pan Du440
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Answer: A: Inquiry about lumiT function
... Hi Neagu You are correct: in formula:h=1/c1*arcsinh⁡(c2/√c3+(c1*m)/√c3), where m represents the mean of the beads values of the probe and h represents the output of lumiT for that probe. For more details, please check the method paper: http://nar.oxfordjournals.org/content/36/2/e11.long Pan ...
written 4.8 years ago by Pan Du440
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Comment: C: methyAnalysis error
... Thanks! Martin The bugs are due to the changes of other depended packages. I have submitted the bug fix to the released version. Hope this will solve problems. Pan On Wed, Nov 13, 2013 at 7:29 AM, Martin Morgan wrote: > On 11/12/2013 11:11 PM, Pan Du wrote: > >> Hi Juan >> > ...
written 4.9 years ago by Pan Du440
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Comment: C: methyAnalysis error
... Hi Juan You need to try the latest developing version of methyAnalysis package. For some unknown reason, the Bioc reports some checking error of the vignette. So the latest developing version is not available through biocLite. It will send the package to you in another email. Thanks for reporting t ...
written 4.9 years ago by Pan Du440
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Answer: A: methyAnalysis error
... Hi Juan I believe the problem was due to the recent update of genoset package. I will further check it. Also can you try using "FDb.InfiniumMethylation.hg19" library instead of " IlluminaHumanMethylation27k.db". "IlluminaHumanMethylation27k.db" and " IlluminaHumanMethylation450k.db" libraries will ...
written 4.9 years ago by Pan Du440
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Answer: A: methyAnalysis error
... "FDb.InfiniumMethylation.hg19" On Fri, Nov 8, 2013 at 2:28 AM, jfertaj wrote: > Dear list > > I’m trying to convert a MethyLumi object into a GenoSet object, but when I > try the following command I got an error: > > > methyGenoSet <- MethyLumiM2GenoSet(filt, > lib="Il ...
written 4.9 years ago by Pan Du440
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Answer: A: Lumi failed to load
... Hi Hitoshi Based on the information you provided. I believe the problem happens when you loading the methylumi package. So please check whether methylumi package was properly installed. If the problem still exists, please provide your sessionInfo(). Pan On Fri, Oct 11, 2013 at 3:00 AM, wrote: ...
written 5.0 years ago by Pan Du440

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