Table 4. Evaluation of different normalization processes.

To this end, microarray data for diseased vs. healthy samples was used and compared with respect to No. of down-regulated scFvs antibodies and No. of complete matches per target molecule, using a fold change (FC) filter of either FC > 1 or FC > 1.1 and with and without a cut-off value of q <0.05.

Diseased vs. Healthy	Subtract by group mean + semi-global norm	ComBat norm + semi-global norm	Global VSN + Combat norm	Global LOESS + Combat norm
No. of down-regulated scFvs at FC > 1	38 of 195	37 of 195	91 of 195	99 of 195
No. of down-regulated scFvs at FC > 1 and q <0.05	21 of 151	20 of 150	58 of 135	61 of 119
No. of down-regulated scFvs at FC > 1.1 and q <0.05	21 of 146	20 of 145	53 of 125	57 of 108
No. of complete matches* per target molecule (ntotal = 47)	32	33	23	21

* Each protein analyte was targeted by 2–9 individual scFv clones. A complete match is defined as when all scFvs per target gave similar results with respect to up- vs. down regulations, using a fold change (FC) filter of FC > 1.