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.