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MS Proteomics - Software and Tools - DAnTE

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:

  1. Install the .NET framework 2.0 (from Microsoft) if you don't have it already.
  2. 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"
  3. 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

Software Details
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.

 

DAnTE Feature Tour

Application window

DAnTE GUI

(+) Zoom or View full

Main graphical user interface for DAnTE

 

Correlation Heatmap

Heatmap

(+) Zoom or View full

Heatmap of the similarity of each dataset against all other datasets

 

Boxplots

Boxplots

(+) Zoom or View full

Boxplot display of the range of abundance values within each dataset.

 

Peptide to Protein Rollup

Abundance Rollup

(+) Zoom or View full

Rollup peptide abundances to compute protein abundance estimates

 

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