This chapter explores measurements from an experiment with a batch effect induced by switching the mass of RNA analyzed from 400 ng to 200 ng. The experiment has as additional factors the RNA material (liver, kidney, and two mixtures) and the RNA source (six different animals). We show that normalization can partially correct the batch effect, and that, after normalization, the size of the batch effect is comparable to the animal-to-animal variation. In addition, we present data analysis results that suggest other batch effects.
Citation: Batch effects and experimental noise in Microarray Analysis: sources and solutions
Publisher Info: John Wiley & Sons, Ltd, West Sussex, PO19 8SQ, -1
Pub Type: Book Chapters
biological variation, gauge repeatability and reproducibility, high dimensional, measurement protocol, metrology, mixed-effects model.