Comparison of Merging and Meta-Analysis as Alternative Approaches for Integrative Gene Expression Analysis

Table 3

Number of differentially expressed genes (DEGs) for all merged data sets.

BERM^(i)	No. of DEGs^(ii)	No. of DEGs	No. of DEGs^(iii)
		(resamp.)	(intersection)
NONE	131	112	102
BMC	124	109
COMBAT	125	110
DWD	125	111
XPN	143	123

⁽ⁱ⁾BERM: batch effect removal method. ⁽ⁱⁱ⁾Number of DEGs found on the complete data set without resampling. ⁽ⁱⁱⁱ⁾Number of DEGs in the intersection of the DEG lists for all batch effect removal methods after using resampling.