R help - Sep 2011 - how to get a row with its its p value below 0.01 ??

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...

-- 
******************************************************************
Anand M.T
School of Biotechnology (Bio-Informatics),
International Instituteof Information Technology (I2IT),
P-14, Rajiv Gandhi Infotech park,
Hinjewadi,
Pune-411 057.
INDIA.

"The secret of success comprised in three words.. Work, Finish &
Publish" -
Michael Faraday

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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