2.5 View menu

The View menu options are used to modify the view of genes visible in the pseudoarray image. Genes may be displayed with additional properties or capabilities including access to Web-based genomic database entries for specific genes. Note that depending on your particular database, if some genomic identifiers are not available then the corresponding "Enable display current gene in genomic DB Web browser" will not appear in the menu.

Example of View Menu

Figure 2.5 View Menu options. These are divided into various options for modifying the presentation as well as recording activity such as the messages or history popup scrollable log windows.

A) Example of UniGene popup Web browser page for current gene

B) Example of NCI/CIT mAdb popup Web browser page for current gene

C) Example of LocusLink popup Web browser page for current gene

Figure 2.5. Popup genomic browser database page. A) The UniGene Web page pops up in a new Web browser window when the user clicks on a gene in the array image, 2D scatter plot or Report and the view is set to "Display current gene in Unigene Web Browser" toggle was enabled in the View menu. The current gene was "Jun-B oncogene". Alternatively, the B) mAdb Gene DB may be selected - as well as GenBank or dbEST genomic databases. C) Alternatively, data from the NCBI LocusLink database may be accessed if either the GenBank ID or LocusID is available.

2.5.1 Logging MAExplorer messages

MAExplorer shows various data measurements as well as many other types of information in the three text lines in the status area of the main window. The Show log of messages pops up a scrollable log of all messages to the three line status area. This is useful for recording measurements and other activity. The messages may be saved in log file (typically maeMessages.log). Figure 2.5.2 shows an example of the messages popup log window. Clicking on genes in the pseudoarray image or in plots will log the gene data (
see Section 3.3) given the current normalization, Samples use (single or multiple), and pseudoarray display mode. The current values of all of the State Threshold scrollers are saved in the message log when the (Edit menu | Preferences | Adjust all Filter threshold scrollers) State Thresholds popup window is closed. This is useful for capturing the current settings at any time.

2.5.2 Logging command history

During a datamining session, the user will typically execute many commands from the menu as well as clicking on genes in the pseudoarray image or in plots. It is useful to recording the steps you took during this analysis. The Show log of command history pops up a scrollable history of all commands issued to MAExplorer. The commands are automatically numbered. The history may be saved in log file (typically maeHistory.log). Figure 2.5.2 shows an example of the command history popup log window.

Examples of messages and command history popup log windows

Figure 2.5.2 Examples of messages and command history popup log windows. Measurements and other activity are shown in more detail in the messages window whereas the command history indicates commands (numbered in the order they are executed) in the command history window. Data from either of these windows may be saved in text log files.