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".