P-GSE20296-6 - P-GSE20296-6

Scanning was performed with ScanArray 5000 (GSI Lumonics) and images were processed with GenePix Pro 5.0 (Axon). The measurements in spots were filtered by criteria I/B ≥ 3 and (I-B)/(SI + SB) ≥ 0.6, where I and B are the mean signal and background intensities and SI, SB are the standard deviations. After subtraction of median background from median signal intensities, the expression ratios (ER) were calculated. Locally weighted non-linear regression (Lowess) normalization was performed, first for the whole slide and next for twelve rows and four columns per slide. The differential expression was assessed by the difference of the mean log2 expression ratios between the slides with reverse labelling (6 spot replicates per gene on each slide, Student´s t-test, p < 0.01). The log2 ER ranked up or down-regulated genes were analyzed interrogating the functional classes of Gene Ontology (GO) and compared by the sums of ranked genes (Student's t-test, p < 0.05).
Experiment E-GEOD-20296