Table 1 Comparison of BART and leading microarray analysis tools with respect to accepted input, data visualization options, and differential expression/post-processing options
Accepted Inputs | QC Plots | Batch | Differential Expression Test | Functional Enrich. Analysis | |||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
GEO CEL files | Expression Table | User Table | GEO DataSet | Volcano Plot | PCA Plot | Heatmap | Box Plots/Bar Graphs | ||||
BART | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | Limma | KEGG |
GEO2R | ✗ | ✓ | ✗ | ✓ | ✗ | ✗ | ✗ | ✓ | ✗ | Limma | ✗ |
GEO2Enrichr | ✗ | ✓ | ✓ | ✓ | ✗ | ✓ | ✓ | ✗ | ✗ | Characteristic direction or t-test | Enrichr |
shinyGEO | ✗ | ✓ | ✗ | ✓ | ✗ | ✗ | ✗ | ✗ | ✗ | t-test, one gene at a time | ✗ |
GDS Tools | ✗ | ✗ | ✗ | ✓ | ✗ | ✗ | ✓ | ✓ | ✗ | Two-tailed or one-tailed t-test, Value means difference, Rank Means Difference | FLink |