Data preprocessing and data analysis

For preprocessing of Affymetrix GeneChip® microarray data various algorithms exist, for example MAS, RMA and GCRMA (10-12). For a detailed discussion of normalization algorithms see Chapter 17. See Chapter 18 for approaches to detect differentially expressed genes, Chapter 19 for clustering algorithms and Chapter 20 for approaches to detect patterns in time course series. Several online tools are available to analyze microarray data from plants (Table 9.1). Data from completed microarray experiments should be submitted to public data repositories (e.g. ArrayExpress, GEO) but also to plant specific microarray databases (e.g. Genevestigator, NASCArrays, TAIR).

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