P-GSE48279-1 - P-GSE48279-1
normalization data transformation protocol
Quantile normalization and subsequent data processing was performed using Agilent Feature Extraction software (version 10.7.3.1) and the GeneSpring GX v11.5.1 software package (Agilent Technologies). After quantile normalization of the raw data, then genes that at least 5 out of 6 samples have flags in Detected (“All Targets Value”) were chosen for further data analysis. Please note: Two raw data files, Sample 1 and Sample 3, contain raw data hybridized to the Agilent-014879 Whole Rat Genome Microarray 4x44K G4131F (Probe Name version) array. The raw data file of Sample 2 is from a later batch and contains raw data from the Agilent-028282 Whole Rat Genome Microarray 4x44K v3 (Probe Name version). The ProbeNames in the Sample data table are from a median merger of each probe in both arrays according to the GenBank Accession numbers. Then the arrays are quantile standardized. So the ProbeNames in the matrix are the names that were merged for the same GenBank Accession corresponding to the later edition of the Agilent microarray probes names. ID_REF = VALUE = log2 value of normalized intensity.