User: Yuan Tian

gravatar for Yuan Tian
Yuan Tian40
Reputation:
40
Status:
New User
Location:
London
Website:
http://www.picb.ac.cn/...
Last seen:
13 hours ago
Joined:
1 year, 1 month ago
Email:
t**************@live.com

Posts by Yuan Tian

<prev • 21 results • page 1 of 3 • next >
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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 6 days ago by Yuan Tian40
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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 13 days ago by Yuan Tian40
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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 13 days ago by Yuan Tian40
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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 13 days ago by Yuan Tian40
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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 8 weeks ago by Yuan Tian40
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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 9 weeks ago by Yuan Tian40
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Answer: A: Bug: QC.GUI heatmap shows wrong column label order
... Hello Hilmar:   You may check this link to see if your error is this, I checked you sessionInfo and which shows you are using plotly 4.5.6. Which is not supported by ChAMP for now. Actually...I thought you can not plot most figures, not only heatmap on your current computer. As I right? Best Yu ...
written 10 weeks ago by Yuan Tian40
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Answer: A: dmrcate(): Error in `$<-.data.frame`(`*tmp*`, "sig", value = logical(0)) : repla
... Hello  Eugene,Tim: I encountered the same error report as well. And I checked it in DMRcate code (I am using version 1.10.0): I think there is a small bug in dmrcate() function. In the function, pcutoff parameter is used to select significant differential CpGs. It can be assigned as value or "fdr" ...
written 3 months ago by Yuan Tian40
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Answer: A: Error using Bumphunter and Block finder using CHAMP
... Hello: Based on your message from ChAMP, I think maybe there is something with the rowname of your beta matrix. Because there is message here : "According to your data set, champ.DMR() detected 0 clusters contains MORE THAN 7 probes within300 maxGap. These clusters will be used to find DMR". Normal ...
written 3 months ago by Yuan Tian40
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Answer: A: Error while using ChAMP
... Hello:   Thanks for using ChAMP for your analysis. To be honest, I don't suggest scientist use champ.process() to analysis Methylation Array, because you can not know the problem and result for each step. Thus I suggest you to use separate steps: champ.load(), champ.QC(), champ.norm()... to analys ...
written 4 months ago by Yuan Tian40

Latest awards to Yuan Tian

Scholar 6 days ago, created an answer that has been accepted. For A: champ.impute doesn't update beta matrix

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