R version 2.9.2 (2009-08-24)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

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 - MKL libraries for acclerated math installed: see help (setMKLthreads)
 - ParallelR packages installed: see help (package='foreach')

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> png(filename="affy-quality-lymph.r%02d.png")
> 
> ## 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)
        a         b         c         d         e         f         g         h 
 68.18425  67.34494  42.12819  61.31731  53.64844 128.41264  49.39112  49.25758 
> ## scale factors, should be within 3x each other. f and g look bad
> sfs(Data.qc)
[1]  9.765986  4.905489 10.489529  7.053323  7.561613  2.475224 13.531238
[8]  8.089458
> ## are we missing lots of samples
> percent.present(Data.qc)
a.present b.present c.present d.present e.present f.present g.present h.present 
 21.65158  26.53124  25.58181  23.53279  23.35615  25.25061  17.96423  24.40274 
> ## 3/5 ratios...
> ratios(Data.qc)[,1:2]
  actin3/actin5 actin3/actinM
a     0.9697007    0.12291462
b     0.3235390   -0.19439139
c     0.4661537   -0.14331962
d     1.2567868    0.15861351
e     0.6036608    0.02095918
f     0.6715308    0.02916033
g     0.3798125   -0.15918419
h     0.4850414   -0.17911051
> 
> 
> warnings()
NULL
>