User: AST

gravatar for AST
AST50
Reputation:
50
Status:
New User
Location:
INDIA
Last seen:
2 years, 5 months ago
Joined:
3 years, 11 months ago
Email:
a***************@ccmb.res.in

Posts by AST

<prev • 15 results • page 1 of 2 • next >
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Answer: A: error when running champ.CNA command
... I guess, because your file name and row names are same the function is giving the error. Please try using a different name for your file. ...
written 3.1 years ago by AST50
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Comment: C: Method for batch correction
... Thank you Vegard. The article surely is very helpful in this regard. ...
written 3.3 years ago by AST50
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Comment: C: Method for batch correction
... Thank you Evan. Will try to follow your suggestion to see if there are any significant differences in my results. ...
written 3.3 years ago by AST50
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Comment: C: Method for batch correction
... Thanks Aaron, I was also doubting that it has to do with the residual D.f. Thanks once again for clarifying. ...
written 3.3 years ago by AST50
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Comment: C: Method for batch correction
... The only part I didn't understand (as he also didn't elaborate it) in that comment is: how does it make difference, if I remove batch first, then adjust for covariates while doing differential analysis? Also, I have seen many people used limma function removeBatchEffect() to remove batch prior to a ...
written 3.3 years ago by AST50
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Method for batch correction
... Hi, I have been using Combat to correct the batch effect in 450k data (~10 batches). Recently, I read an old reply from Dr. Peter Langfelder where he mentioned that  "ComBat should NOT be used before running association testing (lmFit); association testing should be run with batch as a covariate on ...
limma sva combat written 3.3 years ago by AST50 • updated 3.3 years ago by Vegard Nygaard110
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Comment: C: Further analysis of methylation microarrays data (Illumina - idat) after reading
... There are various packages available: minfi, RnBeads, ChAMP, you can use anyone of them whichever suits your method of analysis. ...
written 3.3 years ago by AST50
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Comment: C: Adjustment of covariates in 450k data using Limma
... I am really sorry, I just mixed up two different analysis codes. Actually, in this case I am not subsetting any coefficient. But the question about Method-2 is why can't we find the best fit model for all the covariates and subtract the resulting coefficient from raw methylation values and then use ...
written 3.3 years ago by AST50
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Adjustment of covariates in 450k data using Limma
... Before finding DMPs from 450k data, it is suggested to adjust the data for various covariates like cell count etc. From various forums and literatures, I have come to know there are two methods to adjust the covariates: Method 1: fit <- lm (outcome ~ exposure + covariate) group <- factor( ...
limma 450k covariates written 3.3 years ago by AST50
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Comment: C: How to remove unwanted probes before normalization in 450k data
... Hi James, I have included the script and the error code here. ...
written 3.3 years ago by AST50

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