In [1]:

    

## Most code is commented in this cell since it is unnecessary and time-consuming to run it everytime.
# options(repos='http://cran.rstudio.com/') 
# source("http://bioconductor.org/biocLite.R")
# biocLite("golubEsets")
suppressMessages(library(golubEsets))
#Training data predictor and response

data(Golub_Train)
golub_train_p = t(exprs(Golub_Train))
golub_train_r =pData(Golub_Train)[, "ALL.AML"]
#Testing data predictor
data(Golub_Test)
golub_test_p = t(exprs(Golub_Test))
golub_test_r = pData(Golub_Test)[, "ALL.AML"]

# Thresholding
golub_train_pp = golub_train_p
golub_train_pp[golub_train_pp<100] = 100
golub_train_pp[golub_train_pp>16000] = 16000

# Filtering
golub_filter = function(x, r = 5, d=500){
    minval = min(x)
    maxval = max(x)
    (maxval/minval>r)&&(maxval-minval>d)
}
index = apply(golub_train_pp, 2, golub_filter)
golub_index = (1:7129)[index]
golub_train_pp = golub_train_pp[, golub_index]

golub_test_pp = golub_test_p
golub_test_pp[golub_test_pp<100] = 100
golub_test_pp[golub_test_pp>16000] = 16000
golub_test_pp = golub_test_pp[, golub_index]

# Log Transformation
golub_train_p_trans = log10(golub_train_pp)
golub_test_p_trans = log10(golub_test_pp)

# Normalization
train_m = colMeans(golub_train_p_trans)
train_sd = apply(golub_train_p_trans, 2, sd)
golub_train_p_trans = t((t(golub_train_p_trans)-train_m)/train_sd)
golub_test_p_trans  = t((t(golub_test_p_trans)-train_m)/train_sd)
save(golub_train_p_trans, golub_test_p_trans, golub_train_r, golub_test_r, golub_train_pp, golub_test_pp,"DP.rda")


    

    




Error in save(golub_train_p_trans, golub_test_p_trans, golub_train_r, : object ‘DP.rda’ not found
Traceback:

1. save(golub_train_p_trans, golub_test_p_trans, golub_train_r, 
 .     golub_test_r, golub_train_pp, golub_test_pp, "DP.rda")
2. stop(sprintf(ngettext(n, "object %s not found", "objects %s not found"), 
 .     paste(sQuote(list[!ok]), collapse = ", ")), domain = NA)

In [ ]: