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How to extract x rows to get x pvalues using t.test
2 messages · Jagarlamudi, Choudary, Adaikalavan Ramasamy
You will need to _apply_ the t-test row by row.
apply( genes, 1, function(x) t.test( x[1:2], x[3:4] )$p.value )
apply() is a C optimised version of for. Running the above code on a
dataset with 56000 rows and 4 columns took about 63 seconds on my 1.6
GHz Pentium machine with 512 Mb RAM. See help("apply") for more details.
Regards, Adai
On Tue, 2005-03-15 at 11:59 -0600, Jagarlamudi, Choudary wrote:
Hi all,
My data
genes
[,1] [,2] [,3] [,4]
[1,] 25 72 23 55
[2,] 34 53 41 33
[3,] 26 43 26 44
[4,] 36 64 64 22
[5,] 47 72 67 34
stu<-t.test(genes[,1:2],genes[,3:4])
stu$p.value
[1] 0.4198002 i get 1 pvalue for the entire col1:col2 Vs col3:col4. I am trying to get 5 p values for the 5 rows i have. I am trying to avoid a for loop coz my actual data has 56000 rows and its taking more than 4 minutes to compute. Thanks in advance. Choudary Jagarlamudi Instructor Southwestern Oklahoma State University STF 254 100 campus Drive Weatherford OK 73096 Tel 580-774-7136 [[alternative HTML version deleted]]
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