One statistical point beyond A.K.'s well done response.  As you should well
know, Kruskal-Wallis is a non-parametric equivalent of ANOVA.  However, you
only have two groups and do not require an ANOVA approach.  You could
simply use a Mann-Whitney U (aka.. independent Wilcoxon) test using
wilcox.test().

Charles

On Mon, Apr 15, 2013 at 8:23 AM, arun <smartpink111@yahoo.com> wrote:

> Hi,
>
> set.seed(25)
>  myFile1<-as.data.frame(matrix(sample(1:40,50,replace=TRUE),nrow=10))
>  row.names(myFile1)<- LETTERS[1:10]
> groups <- rep (0:1, c(3,2))
> kruskal<-apply(myFile1,1,kruskal.test,groups)
>  p_kruskal <- sapply(kruskal, function(x) x$p.value)
>  p_kruskal
> #         A          B          C          D          E
> F          G
> #0.08326452 0.08326452 0.56370286 0.56370286 0.24821308 1.00000000
> 0.08326452
>  #        H          I          J
> #1.00000000 0.37425932 0.56370286
> #or
>  sapply(seq_len(nrow(myFile1)),function(i)
> kruskal.test(unlist(myFile1[i,]),groups)$p.value)
>  [1] 0.08326452 0.08326452 0.56370286 0.56370286 0.24821308 1.00000000
>  [7] 0.08326452 1.00000000 0.37425932 0.56370286
> A.K.
>
> ----- Original Message -----
> From: Chintanu <chintanu@gmail.com>
> To: R help <r-help@r-project.org>
> Cc:
> Sent: Monday, April 15, 2013 1:18 AM
> Subject: [R] Kruskal-Wallis
>
> Hi,
>
> I have got two groups of samples; and for every row, I wish to calculate
> Kruskal-Wallis' p-value.
> In the example below, and the stars (****) show where I am struggling to
> design and put things together. Any help would be appreciated.
>
>
> myFile <- data.frame(Sample_1a = 1:10, Sample_1b = 2:11, Sample_1c = 3:12,
> Sample_2a=4:13, Sample_2b=7:16, row.names=LETTERS[1:10])
>
> groups <- rep (0:1, c(3,2))
>
> kruskal <- apply(myFile [1:nrow(myFile),], 1,  kruskal.test, ******)
>
> p_kruskal <- sapply(kruskal, function(x) x$p.value)
>
> Thanks,
> Chintanu
>
>     [[alternative HTML version deleted]]
>
> ______________________________________________
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> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
>
> ______________________________________________
> 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.
>



-- 
Charles Determan
Integrated Biosciences PhD Student
University of Minnesota

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