R help - Nov 2010 - Wilcoxon Rank Sum in R with a multiple testing correction

Hi there,
I'm a total newbie to R. I'd like to use a Wilcoxon Rank Sum test to
compare
two populations of values. Further, I'd like to do this simultaneously for
114 sets of values. The two populations are C and N. The different sets of
values have arbitrary names (I'll call them a, b, c etc). The set-up is as
follows:
     a     b     c     d     ....
C   2
C   3
C   5
C   9
C   4
C   5
.
N   13
N   16
N   18
.

Can someone please show me how to read the data in, do the test on each set
(a, b, etc) and then do, for example, a Benjamani and Hochberg correction
for multiple tests?

That would be great!
Cheers

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For the BH, you can use the command
?p.adjust(..., "BH")

For reading the files in and doing the analysis, here is an example:
http://www.r-tutor.com/elementary-statistics/non-parametric-methods/wilcoxon-signed-rank-test

You'd then need to extract all the P values like this:
x <- wilcox.test(... )
i <- 1 # the place to put the relevant P
P.vector[i] <- x$p.value

There are many ways to perform this, it depends on how your data is
structured (which wasn't fully clear to me from your e-mail)...



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On Wed, Nov 24, 2010 at 3:13 AM, selthy <selthy@hotmail.com> wrote:
>
> Hi there,
> I'm a total newbie to R. I'd like to use a Wilcoxon Rank Sum test
to
> compare
> two populations of values. Further, I'd like to do this simultaneously
for
> 114 sets of values. The two populations are C and N. The different sets of
> values have arbitrary names (I'll call them a, b, c etc). The set-up is
as
> follows:
>     a     b     c     d     ....
> C   2
> C   3
> C   5
> C   9
> C   4
> C   5
> .
> N   13
> N   16
> N   18
> .
>
> Can someone please show me how to read the data in, do the test on each set
> (a, b, etc) and then do, for example, a Benjamani and Hochberg correction
> for multiple tests?
>
> That would be great!
> Cheers
>
> --
> View this message in context:
>
http://r.789695.n4.nabble.com/Wilcoxon-Rank-Sum-in-R-with-a-multiple-testing-correction-tp3056557p3056557.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
	[[alternative HTML version deleted]]

Hi Selthy,
>> I'd like to use a Wilcoxon Rank Sum test to compare two populations
of
>> values. Further, I'd like 
>> to do this simultaneously for 114 sets of values.
Well, you read your data set into R using:

##
?read.table
?read.csv

There are other ways to bring in data. Save the import to a workspace object
at the same time:

myDat <- read.csv (...)

Do the Wilcoxon Rank Sum tests using the implementation of your choice
(there are several):

## See the examples at foot of help page. Lacking data we will make some.
?wilcox.test

pv1 <- wilcox.test(rnorm(10), rnorm(10, 2), conf.int = TRUE)$p.value
pv2 <- wilcox.test(rnorm(10), rnorm(10, 2), conf.int = TRUE)$p.value
pv3 <- wilcox.test(rnorm(10), rnorm(10, 2), conf.int = TRUE)$p.value

Eventually you will discover more elegant ways of assembling a vector (or
some other type of storage object).

Finally, you feed your p-values to:

##
?p.adjust
pAdj <- p.adjust (c(pv1, pv2, pv3), method = c("BH"))

##
?round
?sprintf
cbind.data.frame (Uncorrected = c(pv1, pv2, pv3), BH_Corrected = pAdj)

Eventually you will discover how to turn all of this into an elegant
function. I really do hope that this is not a school assignment. If so....
Well, you still need to do some work to get this going.

Regards, Mark.
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