Clarke Labs

Clarkelabs Microarray Tools

Clarkelabs Microarray Tools New
- WebAffy Tools multiple bioconducotor packages (affy, multtest, annaffy, etc) are used for Affymetrix data analysis and annotation.
- Affymetrix Report Tool extract data from Affymetrix report files, organize it in nice table format; it plots Spike-in Poly-A controls to assess labeling efficiency; it also plot other QC parameters.
- Affymetrix Preprocessing and QA Tool preprocess Affymetrix cel data with RMA, dChip, MAS5 or Our optimized method; it generate a series of advanced diagnostics graphs to assess data at both probe and expression levels; these diagnostics graphs include Histogram, Boxplot, Images of cel data, Scatter Plots, MVA Plots, RNA Digestion Plot, Heatmap of Selected genes, etc.
- Array Visualization tools are to visualize microarray data using Principal Component Analysis (PCA), PCA Movie, Discriminatory Component Analysis (DCA) and Hierarchical Clustering (HC).
- Gene filtering tool This tool is to do gene filtering using various criterions, e.g. t statistics/ANOVA, folder change, exclusion of genes with low intensities.
- Heatmap Tool This tool is to to visualize data with heatmap w/o Hierarchical Clustering.
- FDR/MR Tool This tool is to compute FDR/MR described in the following paper: The 'miss rate' for the analysis of gene expression data. Taylor J, Tibshirani R, Efron B. (PMID: 15618531)
- MLP Prediction tool New This tool is to do class prediction using multiple layer perceptron (MLP).
- IDG/JDG Gene Selection Tool New This tool is to select genes based on IDG/JDG (developed by Dr. Wang's group at CBIL) and multiple layer perceptron (MLP).

Other Tools
- Randomization Plans