User: yuabrahamliu

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Posts by yuabrahamliu

<prev • 8 results • page 1 of 1 • next >
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Comment: C: Use ChAMP to Find Differential Methylation Regions (DMR)
... Hi Yuan, Your suggestion is very helpful! I reduced the number of cores required from 10 to 3, and then it worked smoothly! Although 3 cores will not be enough in the future because I will run on a large number of samples then, I am still very happy now. Thank you so much Yuan! Best wishes, Yu ...
written 5 days ago by yuabrahamliu0
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Comment: C: Bumphunter error: subscript out of bounds
... Hi, I also encountered the same problem. Have your problem been solved? Thank you so much. Best wishes, Yu ...
written 5 days ago by yuabrahamliu0
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Use ChAMP to Find Differential Methylation Regions (DMR)
... Hi there, I always have a bug when use ChAMP to call differential methylated regions (DMR) and I have tried many times but I still cannot get over it, hope someone could give me some help. I used ChAMP to analyze EPIC data and after Combat, I went to the step to find differential methylation probe ...
champ dmr champ.dmr written 5 days ago by yuabrahamliu0
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Comment: C: Some terms in EPIC Methylation Analysis
... Really helpful! Thank you so much! ...
written 6 days ago by yuabrahamliu0
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Some terms in EPIC Methylation Analysis
... Hi there, Maybe this is a silly question, but it really made me confused. When use ChAMP to analyze EPIC methylation data, the SVD step will display the significant components of variation in the result heatmap. The components always include Sample Plate, Array and Slide. However, I don't know exac ...
champ array svd slide sample plate written 6 days ago by yuabrahamliu0 • updated 6 days ago by Yuan Tian40
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Comment: C: ChAMP Normalization on EPIC Methylation Data
... OK. Thank you so much. ...
written 8 days ago by yuabrahamliu0
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ChAMP Normalization on EPIC Methylation Data
... Hi there,  I met a problem when using ChAMP to perform normalization on EPIC data. Actually, SWAN, PBC and BMIP can work well, but when I use FunctionalNormalization  to do that, I always got an Error. My code is,  myNormfn <- champ.norm(beta=myLoad_B$beta,                        rgSet=myLoad_B ...
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Comment: C: ChAMP functional normalization error "subscript out of bounds"
... Hi Laura,  I met the same problem while using FunctionalNormalization, but SWAN, BMIQ and PBC can work fine. Have your problem solved? Thank you so much. Yu ...
written 8 days ago by yuabrahamliu0

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