the Bioconductor package ‘Affy' for R. Normalized Log2 transformed probe intensity Robust Multi-chip Average values were used in differential gene expression analyses and transcripts with significantly altered expression (P⩽0.05) between BP and controls were identified using t-test with R and David software.44 To assess similarities between groups, the Symmetrized Stein Distance was calculated between estimated sample covariance matrices for each sample pair (BP vs control iPSC, BP vs control neurons and iPSC vs neurons). Statistical significance was calculated using the permutation test.45 Validation of the microarray results was performed with TaqMan ‘Assays on Demand' (ABI, Foster City, CA, USA) for seven genes selected based on fold changes between BP and control samples, using the 2−ΔΔCt method.46 Only complete sets of iPSC (3 BP and 3 C patients) and neurons (same 3 BP and same 3 C cell lines from 6 individuals) were analyzed to minimize stochastic changes due to culture conditions.
