| pumaFull {puma} | R Documentation |
Full analysis including pumaPCA and mmgmos/pumaDE vs rma/limma comparison
pumaFull (
affybatch = NULL
, data_dir = getwd()
, load_affybatch = FALSE
, calculate_eset = TRUE
, calculate_pumaPCAs = TRUE
, calculate_bcomb = TRUE
, mmgmosComparisons = FALSE
)
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. |
No return values. Various objects are saved as .rda files during the execution of this function, and various PDF files are created.
Richard D. Pearson
Related methods pumaDE, createDesignMatrix and createContrastMatrix
data(affybatch.example)
varLabels(affybatch.example) <- c("level")
pData(affybatch.example) <- data.frame("level"=c("twenty","twenty","ten")
, "batch"=c("A","B","A"), row.names=rownames(pData(affybatch.example)))
pumaFull(affybatch.example)