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