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:
4 days, 4 hours ago
Joined:
1 year, 6 months ago
Email:
t**************@live.com

Posts by Yuan Tian

<prev • 29 results • page 1 of 3 • next >
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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 4 days 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 12 days 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 16 days 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 28 days 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$Sample_Group,method="DMRcate",arraytype="EPIC") [===========================] [<<<<< ChAMP.DMR START >>&g ...
written 8 weeks ago by Yuan Tian70
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Answer: A: ChAMP filter bug when using beta matrix and pd as input
... Hello:   Yes it's obviously a small bug in champ.filter(). Thanks very much to spot it. I have fixed this bug in current version (2.8.3) ChAMP, it should be online in 24 or 36 hours. I forget that RemainSample is the variable I declared in filterDetP if block. my fix message should be appear on b ...
written 8 weeks ago by Yuan Tian70
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Answer: A: Error in champ.load (v. 2.8.3)
... Hello Rasmus:   Could you show me your csv file? Normally, CSV file for DNA methylation data would have some extra lines ahead. So I firstly detected those lines and skipped them. I guess your csv file is not very typical. By checking your csv file, I may modify the code better. Because I can use ...
written 8 weeks ago by Yuan Tian70
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Comment: C: DMRcate fails in ChAMP package
... Hello Rasmus: This error would happen sometime if user using cpg.annotate() function in DMRcate() function without assign Data Matrix's type —— "Beta" or "M". It would more likely happen to small datasets. I have fixed this problem in new version package (2.6.1). And author of DMRcate will also mak ...
written 4 months ago by Yuan Tian70
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Answer: A: champ.impute doesn't update beta matrix
... Hello:   Can I have your code? I tested the function below, but it seems fine:   In below test, myLoad$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 5 months ago by Yuan Tian70
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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 5 months ago by Yuan Tian70

Latest awards to Yuan Tian

Scholar 4 months ago, created an answer that has been accepted. For A: champ.impute doesn't update beta matrix
Scholar 5 months ago, created an answer that has been accepted. For A: champ.impute doesn't update beta matrix

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