MAExplorer - Microarray Exploratory Data Analysis

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.

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.

Show 'Edited Gene List' [CB] - toggle showing the EGL as magenta boxes in the pseudoarray image. If enabled, genes set by manual selection or as the result of some filtering operations (see Edit menu, the Filter and Clustering)
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Enable display current gene in GenBank Web Browser [RB] - when click on a gene in microarray image or scatter plot to access NCBI data. It will use RefSeqID data if available.
Enable display current gene in dbEST Web Browser [RB] - when click on a gene in microarray image or scatter plot to access NCBI data.
Enable display current gene in Unigene Web Browser [RB] - when click on a gene in microarray image or scatter plot to access NCBI data.
Enable display current gene in mAdb Web Browser [RB] - when click on a gene in microarray image or scatter plot to access NCI/CIT data.
Enable display current gene in LocusLink Web Browser [RB] - when click on a gene in microarray image or scatter plot to access NCBI LocusLink data (by Locus ID if available, and GenBank ID if it] is not).
Enable display current gene in OMIM Web Browser [RB] - when click on a gene in microarray image or scatter plot to access NCBI OMIM data by OMIM ID if available.
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Show Filtered spots in array [CB] - if on, show Filtered genes in the microarray image using circle overlays just outside of each spot. Genes not passing the Filter have no circle.
Gang F1-F2 scrolling [CB] - toggle gang scrolling. If on, gang measure F1 and F2 when click on one of them. If off, only measure only the spot that you click on.
Show mouse-over info [CB] - toggle mouse over. If enabled, report HP or gene details when the mouse is moved over the sample names or spots in the array image or genes in scatterplot or expression profile overlay plot.
Presentation view mode [CB] - toggle presentation mode. If enabled, increase the fonts to 12pt and draw darker circles, squares, and "+" so the display details are easier to see when projecting the display or making slides.
Color scheme (red-green) or dichromasy [CB] - toggle between two color schemes red-green and orange-blue for dichromasy which may be easier for some people.
Show log of messages [CB] - toggle message logging mode. If on, it 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.
Show log of command history [CB] - toggle command history logging mode. If enabled, it pops up a scrollable history of all commands issued to MAExplorer. The commands are automatically numbered. This is useful for recording what steps you took during an analysis. The history may be saved in log file.

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.

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.