Quick Links    

 


  Compatible with standard microarray geometrics
  Automatic, Semi-automatic and Manual gridding
  Re-usable grid protocols
  Normalization
  Intensity extraction
  Export intensity data to MS-EXCEL and ASCII text
  User-configurable values for rejection thresholds of elements
  Facility to invalidate bad elements/spots during image analysis
       
     

  Gene annotation
  Probe annotation
  Microarray annotation
  Import gene/probe annotational data
  Annotational dictionary
  Project-based organization of experiments
  Zooming across annotational data
  Dynamic data filtering
  Links to external database
       
     

  Time series analysis
  Hierarchical Clustering
  K-Mean Clustering
  Replicate analysis within and across microarrays
  Principle Component Analysis (PCA)
  Self Organized Maps (SOM)
  Venn Analysis
  Dynamic selection of query data
  Query builder
  Gene groups for use in analysis
  Probe groups for use in analysis
  Microarray groups for use in analysis
       
     

  Time series analysis
  2D scatter plots
  3D scatter plots
  Dendrogram views for hierarchical clustering data
  Venn Diagrams
  Viewing web links
  Physical microarray slide view
  Graphical element view
  Exports graphs to PDF/ Bitmap format
  Zooming to specific data points
       
     

  Quality statistics
  Quality report for image data
  Quality report for processed data
  Element quality report
       
     

  Context sensitive help
  Project management
  Creating project teams
  User level project privilages
  Central storage of data
  Sharing databases with other users
  Partial support for import/export of MIAME compliant data
 
  M vs A plot
 
  Manual Griding using mouse
     
     

SilicoCyte™ is undergoing continuous development where-in new features are added to the software to make it more robust and comprehensive.

* Key features of SilicoCyte™ v 1.4


Import of Upstream data


Import of Affymetrix data
Import SilicoCyte™ 1.4 supports the import of Affymetrix Single Channel Image Analyzed data exported from Affymetrix MAS Suite 5.0. Data analysis can be performed on such Single Channel Image Analyzed data using SilicoCyte™ 1.4.

Import of GenePix Pro(GPR) data
SilicoCyte™ 1.4 supports analysis and management of dual channel c-DNA microarray i.e. GenePix Pro (GPR) data. SilicoCyte™ allows users to perform advanced queries, statistical analysis, and visualization on the imported data.

GenePix Array List (GAL) file Import


GAL file import feature in SilicoCyte™ 1.4 allows you to create new microarray designs from GAL files. A GAL file provides design information about microarray chip geometry and the gene list corresponding to it. The microarray design created from imported GAL files can be used to create new microarray experiments, and perform image analysis of compatible images.

Lowess method of Normalization


SilicoCyte™ 1.4 offers Robust Locally Weighted Polynomial Regression or Lowess method of normalization. Lowess is a regression based method of normalization to correct the dye biases across the entire range of signal intensities