Help : Advanced Result Search Help
Contents
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
The
Advanced
Results Search, allows you to use various criteria to select
hybridizations (arrays) whose data you wish to view or analyze by
clustering. This help page describes these criteria and how to choose
them.
You can select arrays using any of these three methods:
- 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.
After selecting criteria, choose one of the following options:
- '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.
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