Batch correction of microarray data substantially improves the identification of genes differentially expressed in rheumatoid arthritis and osteoarthritis.

Discussion In the present study, the ComBat method was highly effective in removing batch effects due to different acquiry dates of the microarrays; this was demonstrated by i) unequivocal clustering of the RA and OA patients in the batch-corrected data for almost all time points investigated (shown by hierarchical clustering dendrograms and PCA ); ii) integration of the outlier EB87, resulting in reduced standardized variances for a number of genes; iii) identification of a large number of genes differentially expressed between RA and OA with highly significant p-values (up to 5.31E-25); iv) identification of numerous overrepresented GO terms (with an increased number of members and strongly improved p-values).

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