[R] Chi Square with two tab-delimited text files

[David Barron]

In that case, you can just ignore the expected values and use the
observed values in the chisq.test.  The reason you got a p value of 1
before is because the second argument was ignored, and so you did a
chi square test on the expected values alone.

If you have loaded the obseved values into a matrix y using read.table
as in your first example, then just use chisq.test(y).  But you should
notice that you have a lot of zero cells and so probably lots of small
expected values, which is a problem for the chi square test.



On 26/02/07, Carina Brehony <carina.brehony at zoology.oxford.ac.uk> wrote:
> Hi,
> The files look like below and the rows and columns are numbers of genetic
> types e.g. row1 is type 4; column1 is type A. So for, row1:column1 cell
> there are 78 type 4/type A combinations.  I hope this makes sense!
>
>
>
>         78      500     18      6       0       4       0       1       6
> 1       1       0       0       0       1       0       0       0       0
> 0       1       0       0       0       0       0       2       1       0
> 0       0       1       0       0       0       0       23      0       0
> 0       7       0       0       7       0       0       0       6       0
> 8       0       0       0       0       0       0       14      0       0
> 0       0       0       0       0       0       0       5       0       0
> 0       0       0       0       45      0       0       0       0       0
> 0       0       0       0       0       0       0       3       0       40
> 0       0       0       0       0       0       0       0       0       0
> 0       0       0       12      0       0       0       0       8       4
> 0       0       0       0       0       0       ....etc...
>
>
>
>
>
> -----Original Message-----
> From: David Barron [mailto:mothsailor at googlemail.com]
> Sent: 26 February 2007 12:12
> To: Carina Brehony; r-help
> Subject: Re: [R] Chi Square with two tab-delimited text files
>
> It's a bit difficult to advise without knowing what the rows and
> columns represent, but why not just calculate the statistic yourself,
> given that you already have observed and expected values?  For
> example:
>
> chi2 <- sum((y-x)^2/x)
>
>
>
> On 26/02/07, Carina Brehony <carina.brehony at zoology.oxford.ac.uk> wrote:
> > Yes, I would like to do a goodness-of-fit test.
> >
> > -----Original Message-----
> > From: Petr Klasterecky [mailto:klaster at karlin.mff.cuni.cz]
> > Sent: 26 February 2007 11:50
> > To: Carina Brehony
> > Cc: r-help at stat.math.ethz.ch
> > Subject: Re: [R] Chi Square with two tab-delimited text files
> >
> > Carina Brehony napsal(a):
> > > Hi,
> > > I want to do a chi square test and I have two tab delimited text files
> > with
> > > Expected and Observed values to compare.  Each file contains only the
> > values
> > <snip>
> >
> > There are a lot of chi^2 tests, most of them compare O&E quantities and
> > it is not clear which one you want to use. I'd guess a goodness of fit
> > test, but who knows? See ?chisq.test and the examples given there. It
> > also tells you that the y-argument is ignored if x is a matrix (that's
> > probably the reason why you get different results using read.table and
> > scan).
> > Petr
> > --
> > Petr Klasterecky
> > Dept. of Probability and Statistics
> > Charles University in Prague
> > Czech Republic
> >
> > ______________________________________________
> > R-help at stat.math.ethz.ch 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.
> >
>
>
> --
> =================================
> David Barron
> Said Business School
> University of Oxford
> Park End Street
> Oxford OX1 1HP
>
>


-- 
=================================
David Barron
Said Business School
University of Oxford
Park End Street
Oxford OX1 1HP