[BioC] remove microarray batch effects using Limma

Xie, Zhi (NIH/NHLBI) [E] zhi.xie at nih.gov
Mon Oct 25 20:36:35 CEST 2010

Hi everyone,

I have some microarray data files containing two sets of samples in
normal and disease condition. I have tested that the data also contain
significant batch effects with hybridization time. However, the
positive hits I obtained using the following approaches are very
different (using the same cutoff value in decideTests function). I
think I am supposed to use the first approach but I am surprised to
see a big difference between the two approaches. could anyone help
figure out the reasons?


Zhi Xie


Here eset is the expression dataset after RMA function.

Approach 1:
# Consider batch effects in the model matrix

# fit the linear model

Then I create contrast matrix and compute coefficients and errors
using contrast.fit function
Approach 2:
# remove batch effects first

# only consider normal and disease conditions in the model matrix

# fit the linear model
where eset.rm.batch is the expression dataset containing expression
values from exp.eset.rm.batch table

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