P-GSE42018-8 - P-GSE42018-8
NFI-EnR data were processed using RMA. Gene expression values in the Affymetrix cel files were first background corrected and normalized together using RMA algorithm (Bioconductor R package). Low expression probes (i.e., expression value below 40th percentile in at least 7 out of 8 arrays) were removed. For multiple probes mapping to the same gene, only the probe showing the highest expression change for each gene was retained. Finally, moderated t-statistics and FDR correction (limma R package v.2.15.1.) were used to assess the significance of differential expression. Identical steps for signal normalization, background noise correction and statistical testing were applied to temporal arrays. NFI differentially regulated genes were defined as probes with FDR P-value<0.15 and fold change>1.5. Differentially expressed temporal genes were defined as having probes with FDR P-value<0.1 and fold change>2.