saga_norm uses both, user data and SAGA data to perform quantile normalization. Multiple probes within arrays are averaged.
saga_norm(SAGA_RAW, TEST_RAW, pData.joint, plotnumber = 2)
| SAGA_RAW | SAGA raw data matrix |
|---|---|
| TEST_RAW | Test or sample data in SAGA matrix format |
| pData.joint | joint data matrix (internal SAGA data + sample data) |
| plotnumber | default=2 for t-SNE of SAGA model data + sample; alternative = 1 for quantile normalized boxplot with samples |
eset.rma expression set of normalized array data.