Table 1.
Summary input and output for each application from the Asterias suite.
| Application | Input |
Output |
|
|---|---|---|---|
| Tables and data sets | Figures | ||
| DNMAD | GPR or custom format | Normalized log-ratios; A-values | Diagnostic plots. |
| preP | DNMAD output or EDF1 | Post-processed EDF, summary statistics | |
| Pomelo II | preP output or EDF, class indicator, survival time and status | Differential expression statistics and p-values | Heatmap with gene dendrogram |
| Tnasas | preP output or EDF, class indicator | Error rates, selected genes, stability assessments | Cross-validated error rates vs. number of genes |
| GeneSrF | preP output or EDF, class indicator | OOB predictions, error rates, selected genes, stability assessments | OOB error vs. number of genes, OOB predictions, importance spectrum, selection probability plots. |
| SignS | preP output or EDF, survival time and status; optional validation files. | Single-gene statistics and p-values, CV predictions, model results and parameters, stability assessments | Survival plots, dendrograms, partial-likelihood plots. |
| ADaCGH | preP output or EDF and chromosomal location (e.g. from IDconverter) | Genes and segmented regions, summary statistics | Diagnostic plots, chromosome and genome segmented plots |
| IDconverter | identifiers | Mapped identifiers (gene, clone, protein), chromosomal location, PubMed abstracts, GO terms, pathways. | |
| IDClight | URL2 | Same as IDconverter | |
1
EDF: expression (or genomic) data file. See text for details.