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 ~~Describe affybatch here~~
data_dir ~~Describe data_dir here~~
load_affybatch ~~Describe load_affybatch here~~
calculate_eset ~~Describe calculate_eset here~~
calculate_pumaPCAs ~~Describe calculate_pumaPCAs here~~
calculate_bcomb ~~Describe calculate_bcomb here~~
mmgmosComparisons ~~Describe mmgmosComparisons here~~

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

        data(affybatch.example)
        pData(affybatch.example) <- data.frame("level"=c("twenty","twenty","ten")
            , "batch"=c("A","B","A"), row.names=rownames(pData(affybatch.example)))
        pumaFull(affybatch.example)

[Package puma version 1.2.0 Index]