## we need to load some libraries and do some preparation on the initial data
## sets. the affy library is a set of standard analysis routines. while ALLMLL
## contains the data reported at Mary E. Ross, Xiaodong Zhou, Guangchun Song,
## Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami
## Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing
## (2003) Classification of pediatric acute lymphoblastic leukemia by gene
## expression profiling Blood 102: 2951-2959
library( "affy" )
library( "ALLMLL" )


data( MLL.B )
Data <- MLL.B[, c(2,1,3:5,14,6,13)]
sampleNames(Data) <- letters[1:8]


## these stats are some simple values that can be indicative of problems.
## simpleaffy calculates them all for you
library( "simpleaffy" )
Data.qc <- qc(Data)
## this is average background -- they should all be about the same, f isn't
avbg(Data.qc)
## scale factors, should be within 3x each other. f and g look bad
sfs(Data.qc)
## are we missing lots of samples
percent.present(Data.qc)
## 3/5 ratios...
ratios(Data.qc)[,1:2]