Hi James, I did not say that your question shouldn't be asked. It is valid and I'd sure want to know if it happened to me. I simply meant that the R-help list could a be more appropriate place to ask. I doubt the warning is linked to your getting NAs (which you hadn't mentioned in your previous e-mail). That warning clear well documented in the help page for ks.test. I don't know why you are getting NAs as your answers. I cannot reproduce it with the most recent R version, even if I include NA or NULL values. If you post the exact values (or a small reproducible example) for which this happens, we are more likely to be able to help. Also, please include the output from sessionInfo(). Francois On Thu, 2007-10-18 at 18:52 -0700, James Anderson wrote: > Francois, > > I would not post on Bioconductor list if I can still get some answer > with the warning, I found a bunch of p values are shown as NA, but I > can get values out using matlab, so I am wondering what is the EXACT > reason why it shows as NA. > I am sorry for being off-topic on Bioconductor, it would be great if > you can tell me the R help email list. I just don't know this, right > now Bioconductor list is the only list I am seeking help, thanks. > > James > > Francois Pepin <fpepin at="" cs.mcgill.ca=""> wrote: > Hi James, > > Please note that there is nothing bioconductor specific in > this > question. You might want to use the R-help list instead next > time. You > are more likely to get a useful answer from there and it > reduces the > clutter on this one. > > This being said, a warning is not an error, you should still > get a > result. The warning simply means that the KS test will not > give an exact > pvalue if you have identical values in one (or both) of your > distribution. You still get an estimate that I've found to be > usable > when I've used it. > > Francois > > On Thu, 2007-10-18 at 15:37 -0700, James Anderson wrote: > > Hi, > > > > I am trying to use ks test to do gene selection for > microarray data. > > Suppose A is my matrix with 5000 genes and 60 samples, the > first 30 samples are in class 0, the other 30 samples are in > class 1. > > > > I use the following command to calculate the pvalue for each > gene. > > > > index_class0 = which(ClassLabel == 0) > > index_Class1 = which(ClassLabel == 1) > > PvalsAll <- apply(A, 1, function(x) ks.test(x[index_class0], > x[index_class1], > > exact = NULL)$p.value) > > > > I got some warning message like: > > > > In ks.test(x[index_class0], x[index_class1], exact = NULL) : > > cannot compute correct p-values with ties > > > > but with the same data, I can get some values using matlab > statistics toolbox, does anyone have similar experience? How > to fix this problem? > > > > Many thanks, > > > > James > > > > __________________________________________________ > > > > > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor at stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > __________________________________________________ > Do You Yahoo!? > Tired of spam? Yahoo! Mail has the best spam protection around > http://mail.yahoo.com >