RMA and ComBat for 2 batches with samples in common
1
0
Entering edit mode
grla • 0
@grla-9386
Last seen 8.3 years ago

Hi all,

I have a question concerning microarray normalization followed by batch correction.

I have a single experiment with patient data on two time points and I would like to compute the differential expression between both time points.

The samples were analysed in 2 batches.

Batch 1 contains 32  samples (16 on time point 1 corresponding with 16 on time point 2), batch 2 contains 80 samples (40 on time point 1 corresponding with 40 on time point 2).

8 samples (4 pairs) were measured in both batches.

I would like to normalise my data using RMA, followed by a batch correction based on the 8 samples analysed in both batches using the SVA ComBat function with batch number as covariate.

However, it is not clear to me whether I need to perform RMA on both batches separately or on all data together before executing the ComBat function.

 

Thanks in advance for any help!

microarray normalization sva • 1.7k views
ADD COMMENT
0
Entering edit mode
Jeff Leek ▴ 650
@jeff-leek-5015
Last seen 3.1 years ago
United States

You would run RMA or any other pre-processing software on the entire data set together before applying ComBat or sva. 

ADD COMMENT

Login before adding your answer.

Traffic: 862 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6