[R] how to get a row with its its p value below 0.01 ??

[Rolf Turner]

On 14/09/11 17:49, anand m t wrote:
> Hi all,
>
> I'm analyzing micro array data.. it has produced a file (to be specific
> matrix) withdimension of 35556 2.
> first few lines of the matrix are as below..
>
> probe_name control.fdr.pvals.present
> 10338001 0.000440001
> 10338002 0.000583093
> 10338003 0.000528449
> 10338004 0.000610362
> 10338005 0.000151825
> 10338006 0.0001733
> 10338007 0.000152924
>
> Now, i want only rows whose "control.fdr.pvals.present" values are below
> 0.01.
> How do i that?? Please help me soon...

Your question indicates that your knowledge of R is very limited.
If you are going to analyze micro array data in R, it behoves you
to learn some R.  Read, mark, and inwardly digest ``An Introduction
to R'' (under "Manuals" on the R web page, www.r-project.org).
At the very least.

To answer your question:  If your matrix is named "m" then

     m[m[,2] <= 0.01,]

gives you what you want.  Possibly more perspicuously:

     ind <- m[,2] <= 0.01 # ind is a logical vector of length = nrow(m)
     m[ind,] # This selects those rows of m where ind is TRUE

     cheers,

         Rolf Turner