SAM

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SAM (Significance Analysis of Microarrays)

It is planned to have caGrid service version only.

Dependency:

  • the computation is to be carried out by siggenes R package siggenes

developer's manual of SAM

Using R on c2b2 network

install siggenes from source

  • install multtest first [1]. Start R and enter: 
   source("http://bioconductor.org/biocLite.R")
   biocLite("multtest")
  • Then enter the following command, assuming Z:/siggenes is where the source of siggenes is unzipped to. Succeeded only after I removed man directory of siggenes. Otherwise, there are alway some error messages. 
   install.packages("Z:/siggenes", repos = NULL, type="source")

use siggenes

After installation, you can 

   > library("siggenes")
   > data(golub)
   > sam(golub, golub.cl, B=100, rand=123)
Retrieved from "http://wiki.c2b2.columbia.edu/informatics/index.php/SAM"
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