pumaFull {puma} | R Documentation

## Perform a full PUMA analysis

### Description

Full analysis including pumaPCA and mmgmos/pumaDE vs rma/limma comparison

### Usage

    pumaFull (
            affybatch = NULL
    ,       data_dir = getwd()
    ,       load_affybatch = FALSE
    ,       calculate_eset = TRUE
    ,       calculate_pumaPCAs = TRUE
    ,       calculate_bcomb = TRUE
    ,       mmgmosComparisons = FALSE
    )

### Arguments

`affybatch` | An object of class `AffyBatch`.
`data_dir` | A character string specifying where data files are stored.
`load_affybatch` | Boolean. Load a pre-existing AffyBatch object? Note that this has to be named "affybatch.rda" and be in the `data_dir` directory.
`calculate_eset` | Boolean. Calculate ExpressionSet from `affybatch` object? If FALSE, files named "eset_mmgmos.rda" and "eset_rma.rda" must be available in the `data\_dir` directory.
`calculate_pumaPCAs` | Boolean. Calculate pumaPCA from `eset\_mmgmos` object? If FALSE, a file named "pumaPCA_results.rda" must be available in the `data\_dir` directory.
`calculate_bcomb` | Boolean. Calculate pumaComb from `eset\_mmgmos` object? If FALSE, files named "eset_comb.rda" and "eset_normd_comb.rda" must be available in the `data\_dir` directory.
`mmgmosComparisons` | Boolean. If TRUE, will compare mmgmos with default settings, with mmgmos used with background correction.

### Value

No return values. Various objects are saved as .rda files during the execution of this function, and various PDF files are created.

### Author(s)

Richard D. Pearson

### See Also

Related methods `pumaDE`, `createDesignMatrix` and `createContrastMatrix`

### Examples

    ##      Code commented out to ensure checks run quickly
    #       if (require(affydata)) data(Dilution)
    #       pumaFull(Dilution)

[Package puma version 1.10.1 Index]