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Appendix K Microarray data formats Below you find descriptions of the microarray data formats that are supported by CLC Main Workbench. Note that we for some platforms support both expression data and annotation data. K.1 GEO (Gene Expression Omnibus) The GEO (Gene Expression Omnibus) sample and series formats are supported. Figure K.1 shows how to download the data from GEO in the right format. GEO is located at http: //www.ncbi.nlm.nih.gov/geo/. Figure K.1: Selecting Samples, SOFT and Data before clicking go will give you the format supported by the CLC Main Workbench. The GEO sample files are tab-delimited .txt files. They have three required lines: ^SAMPLE = GSM21610 !sample_table_begin ... !sample_table_end The first line should start with ^SAMPLE = followed by the sample name, the line !sample_table_begin and the line !sample_table_end. Between the !sample_table_begin and !sample_table_end, lines are the column contents of the sample. 540
