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Table 2 Examples of gene pairs correlation changes after batch correction. We illustrate two correlation examples (i) between DYSF and SYNPO2L, where the correlation increases significantly and (ii) between DYSF and SYNPO, where the correlation decreases. Both Spearman and Pearson’s correlations are available to indicate that batch effects are prevalent in both parametric and non-parametric statistics. We see considerable changes on their combined correlation coefficients, which is due to the correction of the variation between studies having been done in different labs by different people. In the case of DYSF - SYNPO2L, originally there seems to be no correlation on the combined samples, despite that a strong positive correlation is observed in each individual series. This bias is removed after batch correction with ComBat, resulting in a positive correlation. The example of the DYSFSYNPO pair shows an initial strong positive correlation before batch correction, while the individual series have mixed positive and negative correlations. Following batch correction this value is reduced

From: MyoMiner: explore gene co-expression in normal and pathological muscle

 DYSF - SYNPO2LDYSF - SYNPO
 Spearman ρPearson rSpearman ρPearson r
Uncorrected−0.050.020.620.53
Batch corrected0.620.650.360.42
GSE478810.60.670.310.39
GSE482780.30.31−0.4−0.08
GSE284220.670.790.640.71
Average of the 3 series0.540.620.210.38