Protocol 34 Data analysis

Image analysis and signal quantification were performed with QuantArray version 2.0 (GSI Lumonics, Oxnard, CA). Background fluorescence was calculated from the fluorescence signal of the negative control genes (the mouse nicotinic acetylcholine receptor epsilon-subunit gene and the mouse glucocorticoid receptor homolog gene) in our RAFL cDNA microarray analysis. To remove the systematic variation, it is necessary to normalize the microarray data (see Chapter 17). Gene-clustering analysis (see also Chapter 19) was performed with Genespring (Silicon Genetics, San Carlos, CA).

Identification of gene expression patterns for a molecular diagnosis of kidney tumors

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