DAnTE

DAnTE helps users to perform various downstream data analysis, data reduction, and data comparison steps. DAnTE includes a graphical environment for visualizing the data during the processing steps. DAnTE can associate one or more "factors" with each dataset, which are then taken into consideration during the data processing. The statistical methods are implemented in R, and the graphical user interface is written in C#, using the R(D)COM server for connectivity. DAnTE is designed to run on Windows XP; there are no immediate plans to support it on Windows Vista.

Features available in DAnTE include:

Comprehensive data loading mechanism

Tabular data from CSV, Excel files (either abundances or expression ratios)
SEQUEST output files for spectral count analysis

Diagnostic plots
- Histograms, boxplots, correlation plots
- Peptide-protein rollup plots
- MA plots, PCA plots, etc.
- Heatmaps with Hierarchical and K-means clustering options
Log transformation
Rolling up peptides to proteins (3 methods are available)
Normalization

LOESS normalization
Linear Regression Normalization
Mean Centering
Median Absolute Deviation (MAD) Adjustment across datasets
Quantile Normalization

Principal Component Analysis
Partial Least Squares Analysis
ANOVA (multi-way, unbalanced, random effects)
Non-parametric tests
Fold Changes
Save results to a session file (extension .dnt)

Dependencies:

DAnTE depends on the following:

.NET framework 2.0 (link)
R software (tested on version 2.6.x and 2.7.x) and a few packages (listed below) (link)
R(D)COM application (link to RSrv250_pl1.exe file)

Installation Procedure:

Recommended: The bundled version (66.4 MB) of the tool includes a setup program that can automatically install these dependancies and a folder containing the R packages required. You can install these packages manually by running R (then menu 'Packages -> Install package(s) from local zip files...') or DAnTE will automatically download and install them when you run DAnTE for the first time (connection to the Internet is required).

Custom: Otherwise, you can install them separately following these steps:

Install the .NET framework 2.0 (from Microsoft) if you don't have it already.
Install the R software from R-project.org or from our server: R-2.7.1-win32.exe (30 MB file)
Install the R(D)COM application from the RCom home page or from our server: RSrv250_pl1.exe (3 MB file)
Download DAnTE and install (when you run DAnTE for the first time it will automatically download and install all the required packages)

Download the Bundle

Download Software Tool

Download Help File

Download Source Code

Version	v1.0	Requirements	R R(D)COM server Microsoft .NET Framework 2.0
Date Updated	August 14, 2008	File Size (Software Tool)	4.6 MB (ZIP)
Registration Required	No	File size (Bundle)	67 MB (ZIP)
Developers	Ashoka Polpitiya	File size (Source Code)	16 MB (ZIP)
Comments	The help file is in the Windows compiled help file format (1.7 MB) There is a tutorial which is a 1.1 MB Powerpoint file See the complete Revision History for a history of changes Supplementary Information on running a simple analysis on a sample dataset (1.6 MB)

R packages used:

DAnTE uses the following R packages; they will be automatically downloaded the first time you run DAnTE:

amap: Another Multidimensional Analysis Package
Cairo: R graphics device using cairo graphics library for creating high-quality bitmap
car: Companion to Applied Regression
nlme: Linear and Nonlinear Mixed Effects Models
outliers: Tests for outliers
fpc: Fixed point clusters, clusterwise regression and discriminant plots
pls: Partial Least Squares Regression (PLSR) and Principal Component Regression (PCR)
MASS: Main Package of Venables and Ripley's MASS
impute: Imputation for microarray data
qvalue: Q-value estimation for false discovery rate control
e1071: Misc Functions of the Department of Statistics (e1071), TU Wien
gplots: Various R programming tools for plotting data
ellipse: Functions for drawing ellipses and ellipse-like confidence regions
plotrix: Various plotting functions
scatterplot3d: 3D Scatter Plot
colorspace: Colorspace Manipulation

Acknowledgment

All publications that utilize this software should provide appropriate acknowledgement to PNNL and the OMICS.PNL.GOV website. However, if the software is extended or modified, then any subsequent publications should include a more extensive statement, using this text or a similar variant:

Portions of this research were supported by the National Institute of General Medical Sciences (NIGMS, Large Scale Collaborative Research Grants U54 GM-62119-02), the NIH National Center for Research Resources (RR18522), and the National Institute of Allergy and Infectious Diseases NIH/DHHS (through interagency agreement Y1-AI-4894-01). Work was performed at Pacific Northwest National Laboratory (PNNL) in the Environmental Molecular Sciences Laboratory, a national scientific user facility sponsored by the U.S. Department of Energy (DOE) Office of Biological and Environmental Research. PNNL is operated by Battelle for the DOE under contract DE-AC05-76RLO-1830.