MarC -V : Microarray Calculation and Visualization
Analysis Tool In a Familiar Excel Format
Download Mac Version (unsupported, less functionality)
Requirements:
Windows NT 4.0/98/2000 professional
Microsoft Excel (MS Office 2000) or newer.
Excel VBA macro add-ins installed (MS Office installer CD)
Function:
Automated analysis of single expression cDNA microarray experiments
Instructions:
Automated Features:
Importing of GenePix-type files (*.gpr). [For GenePix 3.0 or higher] Currently imports mean pixel intensity fields for each array element
Single experiments may be exported to a single text file for use as input in cluster analysis. Expression ratios may be calculated using either the cy3 or cy5 as the denominator.
Removal of elements which are flagged as "bad" (GenePix)
Background subtraction
Thresholding: Your solvent blanks (i.e. DMSO or SSC) are used to calculate a threshold or floor such that no background subtracted values can be less than the calculated threshold.
Calculation of expression ratios, log ratios and fold change for 2 channel (Cy3 and Cy5) experiments. This is best suited for RNA vs. RNA experiments currently. Other types (i.e. RNA vs genomic standard are possible but the normalization calculation should likely be customized to your specifications) are possible.
Normalization: Given the assumption that most of the genes on your array will not be highly regulated in a given hybridization experiment, we normalize such that the sum of all log ratios for an array should be zero.
Generation of plots by pressing a button: a) Frequency distribution of expression log ratios (above), b) Scatter plot of Cy3 vs. Cy5 background subtracted mean pixel intensity values, and c) expression log ratios vs. average intensity for Cy3 and Cy5 channels.
Ratio scoring: Using both proximity to noise and pixel saturation plus actual intensity range
Buttons to sort by: Gene name, log ratio, and ratio score
Worksheet to display most up and down regulated genes
Screenshots:
Normalization 1 Exporter Results Exporter
Frequency Distribution Cy5 vs. Cy3 Scatter Plot
Ratio Score Plot Interesting Genes Worksheet
Future Developments:
Ability to export expression data in a standardized XML format. So far Rosetta's GEML and EBI's MAML are being looked into.
More elaborate filtering methods
Reference:
MarC-V: A spreadsheet-based tool for analysis, normalization, and visualization of single cDNA microarray experiments. Schageman, J.J. M. Basit T.D. Gallardo H.R. Garner and R.V. Shohet. BioTechniques 32:338-344 (February 2002) [PDF]
Contact:
Questions or comments email: Jeff.Schageman@UTSouthwestern.edu
