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The experimental data used in this tutorial was not generated de novo; it came from an existing experiment whose data is publicly available on the official NCI instance of caArray at https://array.nci.nih.gov/caarray/home.action^{Image Removed} (you must have an official NCI user account to access this site). The ID of the experiment from which the data was taken is 'EXP-498'experiment, entitled "TCGA Ovarian: Comparative Genome Hybridization Analysis Using the Agilent Human Genome CGH 244A Platform", was conducted at Harvard Medical School in Boston, MA. It can be accessed via the URL https://array.nci.nih.gov/caarray/project/EXP-498^{Image Added} or by searching for the experiment ID 'EXP-498' on the NCI caArray instance. The array design used was TCGA-Agilent_HG-CGH-244A; the ADF array design files can be downloaded from the experiment, as can all the experiment data, including the IDF and SDRF metadata files, the Agilent TXT raw array data files, and the TSV derived array data files.

Getting Started – Preparing Data for Upload

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