Question: How to remove batch effects using surrogate variables?
1
gravatar for hansong798
19 months ago by
hansong79820
hansong79820 wrote:

My methylation data has about 800 sample and 300,000 variables and I found 26 surrogate variables using 'DoISVA' package in r.

The problem is that r function that remove batch effects like 'removeBatchEffect' or 'ComBat' can get only 1 or 2 batch effect as input. However, in mycase, I want to remove batch effect using 26 surrogate variables.

Is there suitable any r package or other possible way to solve this problem?

R • 472 views
ADD COMMENTlink modified 19 months ago • written 19 months ago by hansong79820

26?! ...do you want to eliminate every last bit of useful information from your data? Why do you feel the need to remove batch effects? - is there genuinely a batch effect (have you checked)?

ADD REPLYlink written 19 months ago by Kevin Blighe67k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1402 users visited in the last hour