Expression Data:
SNP Data: Import Affymetrix SNP array data and link to expression array data
RNA Data: Import Affymetrix whole exon (HuEx, MoEx, or RaEx) array data and link to expression array data. Infer gene expression by mapping exons to known genes from RefSeq and AceView.
µRNA Data:
Methylation Data: Import Infinium DNA methylation data.
Protein Data:
Covariate Data: Import other biological, clinical and/or demographic/descriptive data from an Excel spreadsheet, delimited text files or entered directly with a data editor.
Impute Missing: Impute missing data using a k-nearest neighbor algorithm.
Transformations: Provides a comprehensive set of tools for standardization, normalization, log transform and/or data permutation, including the ability to randomize samples or genes to determine the null distribution of statistics.
Presence/Absence: Assign presence/absence labels using MAS and/or customized P/A calls.
Data Edit: View/edit sample covariate and gene covariate data, gene expression values, their S.E.s and P/A calls. Covariates can be given text labels for easy interpretation.
Recode: Assign values to sample (or gene) covariates based on arithmetic or logical combinations of values of other covariates.
Sort: Multi-key sort of samples or genes.
Labels & Notes: Genes and samples can be conveniently renamed, as required. The sample (or gene) name may incorporate selected covariate information. All projects, samples, genes, gene and sample subsets and meta-cluster analysis files may include a free-format text annotation.
Survival Time Definition: Define right censored outcomes in terms of start and end dates/times and a censor date/time or indicator.
Replicates: Experimental replicates can be combined in a user-specified manner, as can data from multiple probe sets that represent a single gene target.
Subsets: Subsets are used to define sets of genes and/or samples to work with. Genes may be selected on their attributes (e.g. pathway membership, molecular function), quality of the data (e.g. proportion of samples with outliers), cluster membership etc. Samples may be selected according to a covariate value, or randomly chosen (to create a test data set). Venn diagrams permit analysis of the relationship between subsets.
Log: An external XML Log file keeps track of each step in an analysis. This file records screen graphics, gene lists and sample lists and can be viewed and edited using a separate viewer. Displays can be captured into a jpg file or the clipboard or sent directly to a printer.
HTML Output: User-selected portions of the Log can be reformatted as an HTML file for dissemination.
