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