Analysis of prostate cancer serum samples and healthy controls using recombinant antibody microarrays.

Serum samples collected from prostate cancer (PC) patients (nmPC=non-metastatic PC, mPC = metastatic PC) and healthy controls, HC (including the subgroups HC-1 and HC-2) were biotinylated and analyzed using antibody-based microarrays. Along the process, a quality control sample (QCpool) consisting of pooled human serum from five healthy individuals, biotinylated at one occasion, was also included in each assay.In total, 363 serum samples (derived from prostate cancer patients and healthy controls) were analyzed using an antibody microarray consisting of 363 antibodies (scFv). The IMMray Evaluation Software (IES, Immunovia AB, Lund, Sweden) was used to align and quantify spot signal intensities. Using IES, local background was subtracted from each spot signal. Each data-point was represented by a mean spot intensity signal calculated based on three spot replicates per antibody. If the replicate coefficient of variation (CV) exceeded 15% from the mean value, the mean spot intensity was based on the two remaining replicates, which displayed most similar signals. In addition, all mean signals were trimmed, where 5% of the lower and upper extreme values were discarded, leading to the raw data file "Raw data_363 clinical samples and 136 QCpool samples_363 abs". Missing values (noted with NA) were replaced by bagged tree imputation, and acquired mean signal intensities were log2 transformed and normalized using Bayes algorithm ComBat to adjust for batch (print-to-print) variation. This data is available in the file "Normalized log2 data_363 clinical samples_363 abs". In addition, 136 QCpool samples which were analyzed in the antibody microarray were also processed (separately) in a similar way as described above, and the data is available in the file "Normalized log2 _QCpool data".