Computational protocol: Altered Gene Expression in Schizophrenia: Findings from Transcriptional Signatures in Fibroblasts and Blood

Similar protocols

Protocol publication

[…] The oligo package was used to read the CEL files and compute the log intensities of gene expression by exploiting the Robust Multi-array Average (RMA) algorithm. Linear model fitting (LmFit) and the Empirical Bayes method (eBayes) from the BioConductor [] limma package [] were used to test the differences in mRNA levels.The robust empirical Bayes procedure was used to treat outliers []. Only genes with a median of the log2-transformed expression level (ME) higher or equal than 6 were considered for filtering variations in the probe signal due to noise [].The gene lists obtained were filtered using a cut off of p-value < 0.01 and a fold change (FC) of at least ±2 (). Although several statistical tests permit genes with arbitrarily small fold-changes to be considered statistically significant, it has become increasingly common to require that differentially expressed genes satisfy both p-value and FC criteria simultaneously []. The microarray data has been submitted to Gene Expression Omnibus (accession number: GSE62333). […]

Pipeline specifications

Software tools Oligo package, limma
Databases GEO
Application Gene expression microarray analysis
Organisms Homo sapiens