Help : Advanced Result Search Help

Contents

• Description
• Choosing Arrays

Related Help Documents

• Data Selection for Analysis: Explanation of the steps involved in selecting and filtering data for clustering
• Analysis Methods: Information about the algorithms used for hierarchical clustering and Self-Organizing Maps (SOMs)
• File Formats: Information about preclustering (.pcl), clustered data table (.cdt), gene tree (.gtr) and array tree (.atr) files generated in the process of clustering data

Description

Choosing Arrays

• Method 1 allows you to select hybridized arrays by choosing experimenters, categories, subcategories, and/or the organism whose DNA is on the chip. You may select multiple experimenters, categories, and subcategories, but you may only select one organism at a time. The 'Limit Lists by Organism' button will remove all the experimenters, categories, and subcategories that do not have data for the organism you selected.
• Method 2 allows you to select hybridized arrays by the name of the print to which the array belongs.
• Method 3 permits you to set up quick access to a group of hybridized arrays you use frequently. Before you can use this option, you need to create a directory in your home directory named 'arraylists'; see the instructions for details on creating this directory and defining a list of arrays.
  If you create the arraylists directory or a list of arrays while the on the Advanced Results Search page, you need to hit the 'Reload' button to see your file listed on the pull-down menu.

• 'Display Data' will list the arrays that fit your search criteria, including additional information about those hybridizations and links for viewing the experimental data, and images of the hybridized arrays. If you are a local user, you will also be able to edit and delete any of your hybridizations that appear in this list.
• 'Data Retrieval and Analysis' will allow you to select hybridized arrays from a list of those that met your original search criteria. It is also how you should select hybridizations for clustering. Once you have chosen your set of hybridized arrays, you may choose 'Display Data', as described above, or 'Data Retrieval and Analysis' to cluster this data. Chosing 'Create Array List' is one way do define a list of experiments for clustering or data retrieval; see the arraylist instructions for more information on this option.