R help - Nov 2007 - wilcox test on two data frames

Hi all,
 
Basically I have 2 data frames with equal dimension and I want to apply the
wilcox.test to compare columns in the same position (i.e. 1st of df.A with 1st
of df.B, 2nd of df.A with 2nd of df.B,...).
Anyone give me an hint on this, as I think it is nicer to avoid loops, specially
for huge dataframes (30000 x 200)
 
Thanks in advance,
 
Diogo André Alagador
Portugal

	[[alternative HTML version deleted]]

I don't think that the loop-part puts a great penalty in this case; 
however, it'd be better to convert the data.frames to matrices, since 
matrix indexing is faster, e.g.,

# I presume that you only want to keep the p-values
mat.A <- data.matrix(df.A)
mat.B <- data.matrix(df.B)
pvalues <- numeric(200)
for (i in 1:200) {
    pvalues[i] <- wilcox.test(x = mat.A[, i], y = mat.B[, i])$p.value
}


I hope it helps.

Best,
Dimitris

----
Dimitris Rizopoulos
Ph.D. Student
Biostatistical Centre
School of Public Health
Catholic University of Leuven

Address: Kapucijnenvoer 35, Leuven, Belgium
Tel: +32/(0)16/336899
Fax: +32/(0)16/337015
Web: http://med.kuleuven.be/biostat/
     http://www.student.kuleuven.be/~m0390867/dimitris.htm


----- Original Message ----- 
From: "Diogo Alagador" <alagador at oniduo.pt>
To: <r-help at r-project.org>
Sent: Tuesday, November 06, 2007 12:30 PM
Subject: [R] wilcox test on two data frames


Hi all,

Basically I have 2 data frames with equal dimension and I want to 
apply the wilcox.test to compare columns in the same position (i.e. 
1st of df.A with 1st of df.B, 2nd of df.A with 2nd of df.B,...).
Anyone give me an hint on this, as I think it is nicer to avoid loops, 
specially for huge dataframes (30000 x 200)

Thanks in advance,

Diogo Andr? Alagador
Portugal

[[alternative HTML version deleted]]




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On Tue, 6 Nov 2007, Diogo Alagador wrote:
> Hi all,
>
> Basically I have 2 data frames with equal dimension and I want to apply 
> the wilcox.test to compare columns in the same position (i.e. 1st of 
> df.A with 1st of df.B, 2nd of df.A with 2nd of df.B,...). Anyone give me 
> an hint on this, as I think it is nicer to avoid loops, specially for 
> huge dataframes (30000 x 200)
Avoiding loops is unlikely to help with speed. It is more likely to be 
useful to avoid large dataframes (using lists or matrices) but you may 
need the dataframe structure for something else.

If you really want to avoid loops because it is nicer you could use 
mapply():
   mapply(wilcox.test, df.A, df.B)
but this might be slower than a loop.

 	-thomas