Welcome to MeV

Hints and Reminders


Note: Download and Information about the full TM4 Microarray Analysis Suite is available at:

http://www.tm4.org/


An online pdf manual for MeV (this application) is available for viewing at:

http://www.tm4.org/documentation/MeV_Manual.pdf

Hints, Trimming Data

Some large data sets should be trimmed before full analysis begins. This enables memory intensive algorithms (e.g. Hierarchical Clustering (HCL), which works best on sets below about 8,000 genes) to work on a reasonable size data set. The limits depend primarily on available memory. Two primary methods of filtering are available.

Percentage Cutoff Trimming

This will allow the user to insure that there is adequate expression representation for each gene. If gene expression is reported for a gene and for some reason over the set of hybridizations the gene has very few valid values then the gene should probably not enter analysis.

To use this feature select the 'Adjustment' menu and then select 'Set Percent Cutoff'. The resulting dialog will allow you to set a percentage value (0 to 100) describing the percentage of valid values a gene requires in order to pass. Note that all MeV dialogs have an information button in the lower left corner to provide further information. After selecting the cutoff criteria select 'Use Percent Cutoff' from the 'Adjustment' menu. The main view will still show all genes but a subset, reported in the history node on the navigation tree, will describe the number of remaining genes.

Statistical Methods for Trimming

TTEST and SAM (manual sections 9.13 and 9.14) are popular statistical tools that can extract significant genes. Note that after running any algorithm, a right click menu option within cluster viewers, 'Launch New Session', will allow you to open a new viewer containing just the selected genes. This will allow further analysis on a data subset.

Display Options

The 'Display' menu contains many controls that affect the main and cluster viewers. The most frequently used options are 'Element Size', 'Label', 'Set Ratio Scale', and 'Color Scheme'.

The Element Size menu option (of the Display menu), allows one to select the size of each expression element in expression image viewers (e.g. the Main View). Text size in this view is linked to the element height.

The Label menu option allows you select the annotation type to display.

The Set Ratio Scale menu option in the Display menu allows you to adjust the color scale limits to better resolve expression changes in the expression images.

The Color Scheme menu options allow the use of alternate color schemes, such as blue/yellow or a cutomized scheme, if the green/red scale is difficult to resolve.

Final Notes

Please use the pdf manual to explore the various algorithm options and to get a full understanding of MeV's capabilities. The standalone version of MeV is available through the TM4 website above. Thanks for using MeV.