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 <[EMAIL PROTECTED]> 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:[EMAIL PROTECTED] > 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 <[EMAIL PROTECTED]> wrote: > > Yes, I would like to do a goodness-of-fit test. > > > > -----Original Message----- > > From: Petr Klasterecky [mailto:[EMAIL PROTECTED] > > Sent: 26 February 2007 11:50 > > To: Carina Brehony > > Cc: r-help@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@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 ______________________________________________ R-help@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.