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Features of GenePlus™ 1.2

GenePlus™ is a software tool for analyzing gene expression data, a paradigm technology shift from cluster analysis. It facilitates an objective analysis of complex genomic expression data and enables researchers to test specific hypotheses. Version 1.2 is a major upgrade from version 1.1, and includes many significant improvements over the previous version. Here are major highlights:

Application
Time-Course (single series & two series)
Dose-Response
Multiple Group Comparison (two- & multi-groups)
Clinical Studies with Multiple Covariates
Repeated Measurements (Replicates)
Longitudinal Studies with Time-Varying Covariates
Analysis of Two Chips
Analysis of Multiple Pairs of Chips

 

Technologies
Oligonucleotide Data Differences of PM and MM obtained by GeneChip Techology
Ratio data with common reference in Microarray Chip technology
Intensity data obtained by Microarray Chip technology
cDNA Array Data Assembled array data from multiple cDNA array data obtained by microarray technology
Array data obtained from user-chosen image analysis programs
Normalization of array data between two channels

 

Statistical Techniques
Estimating Equations
Bootstrap
Permutations
Use of Standard Statistics (Signals, Standard Deviations, Z-scores and P-values)
Use of NFD(Number of False Discoveries) to measure the significance of discovered gene list
Use of genomewide rankscores
Efficiency and Robustness

 

Heterogeneity Adjustment
Adjustment by correcting means and standard deviations
Parametric Adjustment Additive adjustment
Multiplicative adjustment
Both additive and multiplicative adjustment
Nonparmatric adjustments Additive adjustment
Multiplicative adjustment
Both additive and multiplicative adjustment
Normalization of two chips
Normalization of multiple chips

 

Missing Data
User-defined missing data
Permutations for missing data
Finding and replacing missing values
Incorporating missing values in the analysis

 

Visualization Tools
Click to view it's image ! X-Y plots
Click to view it's image ! Histograms
Click to view it's image ! Chip-Representations
Click to view it's image ! QQ plots
Click to view it's image ! Summary Plot from the Analysis

 

Database Management and I/O
Management of users
Management of data and results
Representation in Spreadsheets
User-Friendly I/O
Versatile interactions with Excel
No limitations in number of genes or number of samples
Import data stored in multiple files

 

Connections with Public Databases
Established connections with Locuslink
OMIN
PubMed
User-specified connections with Any public databases
Any private databases

 

Report Generator
Generating summary reports
Generating reports with discovered information from web

 

Miscellaneous Tools
Transformation Logarithm with a specified base
Exponentiation with a specified base
Box-Cox transformations
Many other functions
Sorting Capacity Sort rows or columns
Sort and save order
Sort by an established order
Editing Function Finding
Copying
Pasting
Interactions with Excel Import from Excel & ASCII Text
Export to Excel & ASCII Text
Cut and paste between GenePlus and Excel & ASCII Text
Manipulating variables Filtering data
Re-coding data
Creating dummy variables
Creating cross-products
Selecting resulting data of interest Selecting a subset of data for further analysis
Identifying candidate gene lists
Comparing candidate gene lists