User: Yuan Tian

gravatar for Yuan Tian
Yuan Tian50
Reputation:
50
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Trusted
Location:
London
Website:
http://www.picb.ac.cn/...
Last seen:
3 days, 20 hours ago
Joined:
1 year, 5 months ago
Email:
t**************@live.com

Posts by Yuan Tian

<prev • 25 results • page 1 of 3 • next >
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Answer: A: error in champ.DMR using DMRcate (v2.8.3)
... Hello Mia: I just tested DMRcate function on a EPIC data on my computer, it seems works fine. Below is my code: ​> myDMR <- champ.DMR(myFilter$beta,pheno=myFilter$pd$Sample_Group,method="DMRcate",arraytype="EPIC") [===========================] [<<<<< ChAMP.DMR START >>&g ...
written 3 days ago by Yuan Tian50
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Answer: A: ChAMP filter bug when using beta matrix and pd as input
... Hello:   Yes it's obviously a small bug in champ.filter(). Thanks very much to spot it. I have fixed this bug in current version (2.8.3) ChAMP, it should be online in 24 or 36 hours. I forget that RemainSample is the variable I declared in filterDetP if block. my fix message should be appear on b ...
written 3 days ago by Yuan Tian50
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Answer: A: Error in champ.load (v. 2.8.3)
... Hello Rasmus:   Could you show me your csv file? Normally, CSV file for DNA methylation data would have some extra lines ahead. So I firstly detected those lines and skipped them. I guess your csv file is not very typical. By checking your csv file, I may modify the code better. Because I can use ...
written 4 days ago by Yuan Tian50
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Comment: C: DMRcate fails in ChAMP package
... Hello Rasmus: This error would happen sometime if user using cpg.annotate() function in DMRcate() function without assign Data Matrix's type —— "Beta" or "M". It would more likely happen to small datasets. I have fixed this problem in new version package (2.6.1). And author of DMRcate will also mak ...
written 12 weeks ago by Yuan Tian50
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Answer: A: champ.impute doesn't update beta matrix
... Hello:   Can I have your code? I tested the function below, but it seems fine:   In below test, myLoad$beta is the 450K dataset included in ChAMP. I used it as an example, we can see that there is no NA in it, so I manually added 2000 NA value in it, then used champ.Impute() function to remove i ...
written 3 months ago by Yuan Tian50
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Answer: A: champ.load getting filtered RGChannelSet
... Hello:   Sorry I just see this. Based on current version of ChAMP, it can not do filtering on rgSet data. I am not sure if minfi provide. I will check if I can code that out and add this feature in future version of ChAMP.   Best Yuan Tian ...
written 3 months ago by Yuan Tian50
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Answer: A: Manhattan plot from ChAMP data
... Hello: Sorry for not including Manhattan plot in it, maybe you can send me a link of paper indicating applying Manhatton plot for DNA methylation data, then I will consider included it in next version package. Also, what data exactly you want to extract from ChAMP? what is chromosome size? ChAMP in ...
written 3 months ago by Yuan Tian50
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Answer: A: DMRcate fails in ChAMP package
... Hello Rasmus: This Error was caused inside DMRcate function, ChAMP used used DMRcate function here. I am about to communicate with the author of DMRcate now since this error already caused my ChAMP paper get rejected... Based on my experience, the bug lines on cpg.annotate.R function, 29 lines. It ...
written 3 months ago by Yuan Tian50
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Answer: A: package 'ChAMP' demo/test code fails at champ.CNA()
... Hello:   ChAMP has been updated to version 2.6 and nearly all code has been recoded. I just know this thread was published two years ago...   Firstly I suggest you use champ functions step by step instead of champ.process() so that we could know which part might be wrong.  Secondly I have teste ...
written 5 months ago by Yuan Tian50
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Answer: A: Plotly uprading issue in ChAMP package
... Hello all:   I have just update ChAMP into version 2.6.0, which included some significant improvement. Merely I make ChAMP support newest plotly now. User don't need to used old version plotly package to run ChAMP anymore. This bug has been fixed. http://www.bioconductor.org/packages/3.4/bioc/vig ...
written 5 months ago by Yuan Tian50

Latest awards to Yuan Tian

Scholar 12 weeks ago, created an answer that has been accepted. For A: champ.impute doesn't update beta matrix
Scholar 3 months ago, created an answer that has been accepted. For A: champ.impute doesn't update beta matrix

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