User: Yuan Tian

gravatar for Yuan Tian
Yuan Tian70
Reputation:
70
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Trusted
Location:
London
Website:
http://www.picb.ac.cn/...
Last seen:
1 month, 1 week ago
Joined:
1 year, 8 months ago
Email:
t**************@live.com

Posts by Yuan Tian

<prev • 31 results • page 1 of 4 • next >
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Answer: A: Analysis of DNA hydroxymethylation
... Hello Sarka: ChAMP indeed provided a way to  assessing hydroxymethylation differences, which is similar to DMP, just another way to implement this function to oxyBS data, Tiffany of ChAMP team also added a small paragraph in vignette to emphasis this. She is currently working on oxyBS data in Cambr ...
written 5 weeks ago by Yuan Tian70
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Comment: C: New version of ChAMP can not proceed through champ.DMP
... Hello Sarka: Sorry I was quite busy last week. First question, since you have only about 56/6 samples in each group, maybe the power of test would not be very strong, so it could be the reason. I still think it resulted from some CpGs with p value very close to 0,05. Since BMIQ use random seed, it' ...
written 7 weeks ago by Yuan Tian70
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Answer: A: New version of ChAMP can not proceed through champ.DMP
... Hello Sharka: I did not change any code in champ.DMP() since version 2.8.7 to version 2.8.9. The error happens when ChAMP want to calculate mean value for each DMP in each group. I suspect the reason is there is only 1 DMP significant, thus code  beta[com.idx, which(pheno == Compare[[i]][1])] Ca ...
written 8 weeks ago by Yuan Tian70
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Answer: A: ChAMP filter removing good samples from different batch of EPIC arrays.
... Hello Sarka: Thanks Kasper for your kind explain. I just modified the code, and make sure ChAMP would do correct calculate for mix array data set. I did not encounter this situation before thus did not consider this fully enough. Pretty sorry for the bug.  I have find a mix-array data set and test ...
written 10 weeks ago by Yuan Tian70
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Answer: A: ChAMP filter removing good samples from different batch of EPIC arrays.
... Hello: I am the developer of ChAMP, and you indeed raised a good question, when I coding ChAMP, I did not consider situation that different arrays might be mixed together. And previous I did not included parameter of minfi Force in ChAMP parameter. I will fix it now. You should see the change in 24 ...
written 10 weeks ago by Yuan Tian70
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Comment: C: Error in champ.load (v. 2.8.3)
... Hello Rasmus:   I think the reason is champ.import() read .csv file from illumina machine, normally those csv files contain some additional information ahead, like date or producer's name. So champ.import() would filter them ahead, then read data. I think your data have been modified before, becau ...
written 12 weeks ago by Yuan Tian70
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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 months ago by Yuan Tian70
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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 months ago by Yuan Tian70
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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 3 months ago by Yuan Tian70
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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 6 months ago by Yuan Tian70

Latest awards to Yuan Tian

Scholar 6 months ago, created an answer that has been accepted. For A: champ.impute doesn't update beta matrix
Scholar 7 months ago, created an answer that has been accepted. For A: champ.impute doesn't update beta matrix

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