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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 (you must have an official NCI user account to access this site). The 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 Removed} 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.

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Back on the 'Manage Data' tab, the remaining files from our upload are one IDF, one SDRF, and 20 TXTs (only the first three of these files is shown below due to space constraints). Note that the status of the TXT file from the screenshot (and of all other TXT files in the list) shows as 'Unknown', which means that caArray did not automatically recognize the file type in this particular case. As a result, we will have to manually specify the file type ourselves by selecting all the TXT files in the list, then clicking the 'Change File Type' button below.

For the particular experiment data in this example, the array data files are in the Agilent Raw TXT format. To specify this, in the 'Manage Files' window shown below, select 'Agilent Raw TXT' from the 'Select New File Type' drop-down list, then click on the 'Save' button above it. (NOTE: Depending on the assay type and array design used in your own experiment, your data may be in a different format, in which you will have to select the appropriate type from the drop-down list, or the file type may be automatically recognized by caArray, in which case you won't have to manually specify the file type yourself.)

Back on the 'Manage Data' window, the status of all the TXT files now shows as 'Agilent Raw TXT', indicating that caArray now correctly recognizes the file type.

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• Upload the ZIP archive to your caArray instance

• Manually Depending on the format of your raw array data, manually specify the file type for the raw TXT array data files, as they are may not automatically recognized by caArray

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