digit precision in p value of rcorr

Hi all,
Sorry about posting a really novice question.
I was able to run rcorr after converting the list to a matrix by your help.
I'm though wondering if there is any way to find out an exact p value as
the output only gave me 0 for P value as shown below.
I've added options(digits=10), which doesn't seem to help at all. Any help
would be appreciated.


P
              D Prime T statistics
D Prime               0
T statistics  0


On Wed, Sep 12, 2012 at 2:19 PM, Jason Love <jason.love1492 at gmail.com>wrote:

thanks all for the prompt answer.
Yes, I need to go through the R tutorial rather than learning a snippet of
codes from googling.


On Wed, Sep 12, 2012 at 11:32 AM, Rui Barradas <ruipbarradas at sapo.pt>wrote:

Hello,

The input must be a matrix, not a list (or its special case data.frame).

Var <- read.table(text="
   D.Prime    T.statistics

1    1.7234e-01     4.926800
2    1.4399e-01     2.892000
3    1.4626e-01     2.642800
4    3.5147e-02     1.112400
5    5.8957e-02     2.723700
", header=TRUE)

# library(Hmisc)
rc <- rcorr(as.matrix(Var), type="pearson")
# from recommended package stats
ct <- cor.test(Var$D.Prime, Var$T.statistics, method = "pearson")

rc$P
                D.Prime T.statistics
D.Prime             NA    0.1101842
T.statistics 0.1101842           NA

ct$p.value
[1] 0.1101842

To the op: you should say which library you are using. Even if Hmisc is a
very popular one.

Hope this helps,

Rui Barradas


Em 12-09-2012 16:10, R. Michael Weylandt escreveu:

  On Wed, Sep 12, 2012 at 4:04 PM, Jason Love <jason.love1492 at gmail.com>

wrote:

Hello,
I'd like to test a significance of two variables in their correlation
using
rcorr, which gave me an error of format incompatibility.
Below are the lines that I typed in the R window and let me know if
anyone
knows how to resolve this.

Var=read.csv("03apr10ab_corr_**matrix_in_overlaps.csv",**header=F)
colnames(Var)=c("D Prime","T statistics")

           D Prime    T statistics
1    1.7234e-01     4.926800
2    1.4399e-01     2.892000
3    1.4626e-01     2.642800
4    3.5147e-02     1.112400
5    5.8957e-02     2.723700


rcorr(Var, type="pearson")

Untested (because I'm still without respectable internet after a move)
I believe rcorr would rather have a matrix than a data.frame(), which
is what read.csv produces, so try

Var <- as.matrix(Var)

or

rcorr(as.matrix(Var), type = "pearson")

  Error in storage.mode(x) <- if (.R.) "double" else "single" :

    (list) object cannot be coerced to type 'double'

This suggests that the input to rcorr is being converted to a double,
which isn't a valid storage.mode change for a list (= data frame).

Cheers,
M

           [[alternative HTML version deleted]]