example+R+session+5-23-12

To import data from a text file type data<-read.table("C:/Documents and Settings/kwhittem/Desktop/temp/data.txt")

To see all of the data stored in the data variable type data and hit enter or type edit(data)

To extract one column or row from data data[,1] This would give you the first column if there is only one column in the file

To adjust all of the p values (if your data contains p values) p.adjust(data[,1],"BH")

This could be stored into another value as well x=p.adjust(data[,1],"BH")

If you want to see all of the values less than a certain value x<0.05

If you want to know the number of samples that are less than a certain value sum(x<0.05)

For some data, I was obtaining adjusted p values that were nearly all uniform or were the same value. This happens when there aren't enough features with low raw p values as explained here: https://stat.ethz.ch/pipermail/bioconductor/2007-September/018978.html