[R] NA in wilcox.test

[Peter Dalgaard]

Michelle Emily DePrenger-Levin wrote:
> Hello,
>
> I'm trying to compare the allozyme data from two taxa. I have several
> columns of data (19 loci) for each species. I want to do a Mann-Whitney
> U-test or the wilcox.test (two sample Wilcoxon). When I try to run my code
> (the first two columns are 1:name of the species, 2:name of individual) I
> get the error message:
>             "Error in wilcox.test.default(CaScSc, CaScCo, alternative = "
> two.sided",  :
>         'x' must be numeric"
>
> I do have several NAs in the data which is all I can figure that is
> non-numeric.
>   
No that's not it.
> Any suggestions as to the problem? Is it a problem with having several
> columns/sets of info for each individual?
>
>   
Yes, that is it. A data frame with 19 variables is not a numeric vector. 
You need to do this column by column, or automate it explicitly via a 
for-loop, or (better) lapply() or maybe mapply().

> Thanks for any help anyone can give (I've also used Arlequin and GDA but
> want non-parametric tests)
>
> Michelle DePrenger-Levin
>
> My code is:
>
> scirconv2 = read.csv("CaScSc070420_2.csv", na.strings="?")
>
>
> CaScSc = scirconv2[1:250,3:21]
> CaScCo = scirconv2[251:475,3:21]
> ScCoMWU = wilcox.test(CaScSc, CaScCo, alternative = "two.sided", mu = 0.5,
> paired = FALSE, exact = NULL, correct = TRUE,
>             conf.int = TRUE, conf.level = 0.95)
>
> some of the data:
>
>     ADH TPI1 TPI2 SOD DIA1 MNR1DIA2 MNR2DIA3 ME AAT1 AAT2 G3PDH SDH SDH2
> PGI2 PGD PGM2 MDH1 MDH3 IDH2
> 251   1    1    1   1    1        1        1  1    1    1     1   1    1
> 2   1    4    1    1    4
> 252  NA   NA   NA  NA   NA       NA        1 NA   NA    2     1   1   NA
> 2  NA   NA   NA   NA   NA
> 253   1    1    1   1    1        1        2  1    1    2     1   1    1
> 2   1    4    1    2    4
> 254   1    1    1   1    1        1        1  1    1    1     1   1    1
> 2   1    4    1    1    4
> 255   1    1    1   1    1        1        2  1    1    2     1   1    1
> 2   1    4    1    2    4
>
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>
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