DAnTE

DAnTE helps users to perform various downstream data analysis, normalization, data reduction, and hypothesis testing 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 statconnDCOM for connectivity.

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
Save results to a session file (extension .dnt)

Installation Information:

DAnTE depends on the following:

.NET framework 2.0 on Windows XP or Vista (link)
R statistical software, version 2.9.x, plus a few packages (listed below)
statconnDCOM (link)

Installation Details:

Follow the steps below to install DAnTE:

Install the .NET framework 2.0 (from Microsoft) if you don't have it already.
Install the latest "R and friends" package from http://rcom.univie.ac.at/download.html or from our server: RAndFriendsSetup_latest.exe (143 MB file).
After installing, verify that R and statconn are installed using "Start->All Programs" or "Start->Programs"
Download and run the DAnTE installer

The DAnTE installer includes the setup program for DAnTE 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 allow DAnTE to automatically download and install them the first time it runs.

Download Software Tool

Download Help File

Download Source Code

Version	v1.2	Requirements	R R(D)COM server Microsoft .NET Framework 2.0
Date Updated	September 2, 2009	File Size (Software Tool)	15.6 MB (ZIP)
Registration Required	No	File size (Source Code)	5.5 MB (ZIP)
Developers	Ashoka Polpitiya
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)

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

amap: Another Multidimensional Analysis Package
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
Hmisc: Harrell Miscellaneous
Cairo: R graphics device using cairo graphics library

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.