I still can't reproduce your example. The aov output gives me the following :
> anova(aov(Intensity ~ Group, data = zzzanova)) Analysis of Variance Table Response: Intensity Df Sum Sq Mean Sq F value Pr(>F) Group 5 98.85 19.771 2.1469 0.07576 . Residuals 48 442.03 9.209 --- Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 Next to that I noticed you have truncated data, which has implications for the analysis as well. If you use a Kruskal-Wallis test, the p-value becomes larger : > kruskal.test(Intensity ~ Group, data = zzzanova) Kruskal-Wallis rank sum test data: Intensity by Group Kruskal-Wallis chi-squared = 6.6955, df = 5, p-value = 0.2443 Which is to be expected, as you have almost 50% truncated data. So a p-value of 0.005 seems very wrong to me. Cheers Joris On Tue, Jul 6, 2010 at 7:11 PM, Amit Patel <amitrh...@yahoo.co.uk> wrote: > Hi Joris > > Sorry i had a misprint in the appendix code in the last email > > datalist <- c(-4.60517, -4.60517, -4.60517, -4.60517, -4.60517, -4.60517, > -4.60517, 3.003749, -4.60517, > 2.045314, 2.482557, -4.60517, -4.60517, -4.60517, -4.60517, 1.592743, > -4.60517, > -4.60517, 0.91328, -4.60517, -4.60517, 1.827744, 2.457795, 0.355075, > -4.60517, 2.39127, > 2.016987, 2.319903, 1.146683, -4.60517, -4.60517, -4.60517, 1.846162, > -4.60517, 2.121427, 1.973118, > -4.60517, 2.251568, -4.60517, 2.270724, 0.70338, 0.963816, -4.60517, > 0.023703, -4.60517, > 2.043382, 1.070586, 2.768289, 1.085169, 0.959334, -0.02428, -4.60517, > 1.371895, 1.533227) > > "zzzanova" <- > structure(list(Intensity = datalist, > Group = structure(c(1,1,1,1,1,1,1,1,1, > 2,2,2,2,2,2,2,2, > 3,3,3,3,3,3,3,3,3, > 4,4,4,4,4,4,4,4,4,4, > 5,5,5,5,5,5,5,5,5, > 6,6,6,6,6,6,6,6,6), .Label = c("Group1", "Group2", "Group3", > "Group4", "Group5", "Group6"), class = "factor"), > Sample = structure(c( 1, 2, 3, 4, 5, 6, 7, 8, 9, > 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, > 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, > 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, > 40,41,42,43,44,45,46,47,48,49,50,51,52,53,54) > )) > , .Names = c("Intensity", > "Group", "Sample"), row.names = > c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", > "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", > "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", > "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", > "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", > "51", "52", "53", "54"),class = "data.frame") > > > Thanks for your reply > > > > > > ----- Original Message ---- > From: Joris Meys <jorism...@gmail.com> > To: Amit Patel <amitrh...@yahoo.co.uk> > Cc: r-help@r-project.org > Sent: Tue, 6 July, 2010 17:04:40 > Subject: Re: [R] Help With ANOVA > > We're missing the samp1 etc. in order to be able to test the code. > Where did you get the other p-value? > Cheers > Joris > > On Tue, Jul 6, 2010 at 3:08 PM, Amit Patel <amitrh...@yahoo.co.uk> wrote: >> Hi I needed some help with ANOVA >> >> I have a problem with My ANOVA >> analysis. I have a dataset with a known ANOVA p-value, however I can >> not seem to re-create it in R. >> >> I have created a list (zzzanova) which contains >> 1)Intensity Values >> 2)Group Number (6 Different Groups) >> 3)Sample Number (54 different samples) >> this is created by the script in Appendix 1 >> >> I then conduct ANOVA with the command >>> zzz.aov <- aov(Intensity ~ Group, data = zzzanova) >> >> I get a p-value of >> Pr(>F)1 >> 0.9483218 >> >> The >> expected p-value is 0.00490 so I feel I maybe using ANOVA incorrectly >> or have put in a wrong formula. I am trying to do an ANOVA analysis >> across all 6 Groups. Is there something wrong with my formula. But I think I >> have made a mistake in the formula rather than anything else. >> >> >> >> >> APPENDIX 1 >> >> datalist <- c(-4.60517, -4.60517, -4.60517, -4.60517, -4.60517, -4.60517, >> -4.60517, 3.003749, -4.60517, >> 2.045314, 2.482557, -4.60517, -4.60517, -4.60517, -4.60517, 1.592743, >> -4.60517, >> -4.60517, 0.91328, -4.60517, -4.60517, 1.827744, 2.457795, 0.355075, >> -4.60517, 2.39127, >> 2.016987, 2.319903, 1.146683, -4.60517, -4.60517, -4.60517, 1.846162, >> -4.60517, 2.121427, 1.973118, >> -4.60517, 2.251568, -4.60517, 2.270724, 0.70338, 0.963816, -4.60517, >> 0.023703, -4.60517, >> 2.043382, 1.070586, 2.768289, 1.085169, 0.959334, -0.02428, -4.60517, >> 1.371895, 1.533227) >> >> "zzzanova" <- >> structure(list(Intensity = c(t(Samp1), t(Samp2), t(Samp3), t(Samp4)), >> Group = structure(c(1,1,1,1,1,1,1,1,1, >> 2,2,2,2,2,2,2,2, >> 3,3,3,3,3,3,3,3,3, >> 4,4,4,4,4,4,4,4,4,4, >> 5,5,5,5,5,5,5,5,5, >> 6,6,6,6,6,6,6,6,6), .Label = c("Group1", "Group2", "Group3", >> "Group4", "Group5", "Group6"), class = "factor"), >> Sample = structure(c( 1, 2, 3, 4, 5, 6, 7, 8, 9, >> 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, >> 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, >> 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, >> 40,41,42,43,44,45,46,47,48,49,50,51,52,53,54) >> )) >> , .Names = c("Intensity", >> "Group", "Sample"), row.names = >> c("1", "2", "3", "4", "5", "6", "7", "8", "9", "10", >> "11", "12", "13", "14", "15", "16", "17", "18", "19", "20", >> "21", "22", "23", "24", "25", "26", "27", "28", "29", "30", >> "31", "32", "33", "34", "35", "36", "37", "38", "39", "40", >> "41", "42", "43", "44", "45", "46", "47", "48", "49", "50", >> "51", "52", "53", "54"),class = "data.frame") >> >> >> >> >> ______________________________________________ >> R-help@r-project.org 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. >> > > > > -- > Joris Meys > Statistical consultant > > Ghent University > Faculty of Bioscience Engineering > Department of Applied mathematics, biometrics and process control > > tel : +32 9 264 59 87 > joris.m...@ugent.be > ------------------------------- > Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php > > > > > -- Joris Meys Statistical consultant Ghent University Faculty of Bioscience Engineering Department of Applied mathematics, biometrics and process control tel : +32 9 264 59 87 joris.m...@ugent.be ------------------------------- Disclaimer : http://helpdesk.ugent.be/e-maildisclaimer.php ______________________________________________ R-help@r-project.org 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.