   wilcox.test(data.matrix[i,] ~ data.cl)$p.value

will return the p.value for row 'i'.

With a loop:

   pv = rep(0,42)
   for (i in 1:42) { pv[i]=wilcox.test(data.matrix[i,] ~ data.cl)$p.value }

Is this what you wanted?

Christophe




On 6/14/07, Booman, M <m.booman@path.umcg.nl> wrote:
>
> Dear everyone,
> I am trying to do a Wilcoxon one-sided test on my gene expression data.
> These are the data i have in R:
> data.matrix (matrix, numeric) containing all gene expression data (42
> rows=genes,  42 columns=tumors), no column header or row names
> data.cl (vector, numeric) consisting of 42 0's and 1's to indicate class 0
> or class 1 for each column in data.matrix
>
> I want to do a Wilcoxon one-sided test on the data from class 0 versus the
> data from class 1, for each row (gene) of the data set.
> My first try:
>
> #to make separate matrices for both classes:
> data.matrix.0 <- data.matrix[,data.cl==0]
> data.matrix.1 <- data.matrix[,data.cl==1]
>
> # to run the wilcox.test function for each row:
> rawp <- apply(data.matrix.0, 1, wilcox.test, y=data.matrix.1,
> alternative="less")
>
>
> The result of printing rawp is:
> $`1`
>
>         Wilcoxon rank sum test with continuity correction
>
> data:  newX[, i] and data.matrix.1
> W = 7585, p-value = 1
> alternative hypothesis: true location shift is less than 0
>
>
> $`2`
>
>         Wilcoxon rank sum test with continuity correction
>
> data:  newX[, i] and data.matrix.1
> W = 6700, p-value = 0.9983
> alternative hypothesis: true location shift is less than 0
>
>
> Etcetera for each row of the data matrix.
> I can get the p value for one row (gene) using:
> rawp.1 <- rawp$'1'$p.value
>
> But how can I get these p-values in one list? I have tried:
> rawp <- NULL
> for (i in 1:42) {
>         a <- paste("'", i, "'", sep="")
>         rawp <- rbind(rawp, test$a$p.value)
> }
>
> but that doesn't work (no errors but rawp stays NULL)
>
> There must be an easier way to do a wilcoxon analysis on a matrix!
> I'd appreciate your help with this...
>
> Marije
>
>
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-- 
Christophe Pallier (http://www.pallier.org)

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