hello all, Quick question, how do I get the p value out of the anova? Thanks, Paul> pb<-aov(as.numeric(diff[5,16:33]) ~ grF) > summary(pb)Df Sum Sq Mean Sq F value Pr(>F) grF 3 2.7860e+10 9.2867e+09 4.2236 0.02534 * Residuals 14 3.0783e+10 2.1988e+09 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1> str(summary(pb))List of 1 $ :Classes 'anova' and 'data.frame': 2 obs. of 5 variables: ..$ Df : num [1:2] 3 14 ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10 ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09 ..$ F value: num [1:2] 4.22 NA ..$ Pr(>F) : num [1:2] 0.0253 NA - attr(*, "class")= chr [1:2] "summary.aov" "listof"> attr(summary(pb), "Pr(>F)")NULL
Yea the anova object seems to be odd. It's not S4 so that's why I tried originally the attr() funtion but.... summary(pb)$Pr(>F) Error: unexpected '>' in "summary(pb)$Pr(>"> summary(pb)$PrNULL> summary(pb)@Pr(>F)Error: unexpected '>' in "summary(pb)@Pr(>"> summary(pb)@Pr(F)Error: no slot of name "Pr" for this object of class "summary.aov" In addition: Warning message: trying to get slot "Pr" from an object (class "summary.aov") that is not an S4 object>Research Programmer & Technician The Scripps Research Institute Mass Spectrometry Core Facility o The / o Scripps \ o Research / o Institute markleeds@verizon.net wrote:> Hi: it's probably the Pr(> F) element so just access it by > > sum<-summary(whatever). > > then sum$Pr(>F) will probably work. But make sure that's it because > usually the name is pval or pvalue etc so I'm > surprised about the weird name. > > > > > On Wed, May 7, 2008 at 8:47 PM, Paul Benton wrote: > >> hello all, >> >> Quick question, how do I get the p value out of the anova? >> >> Thanks, >> >> Paul >> >>> pb<-aov(as.numeric(diff[5,16:33]) ~ grF) >>> summary(pb) >> Df Sum Sq Mean Sq F value Pr(>F) >> grF 3 2.7860e+10 9.2867e+09 4.2236 0.02534 * >> Residuals 14 3.0783e+10 2.1988e+09 >> --- >> Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 >>> str(summary(pb)) >> List of 1 >> $ :Classes 'anova' and 'data.frame': 2 obs. of 5 variables: >> ..$ Df : num [1:2] 3 14 >> ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10 >> ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09 >> ..$ F value: num [1:2] 4.22 NA >> ..$ Pr(>F) : num [1:2] 0.0253 NA >> - attr(*, "class")= chr [1:2] "summary.aov" "listof" >>> attr(summary(pb), "Pr(>F)") >> NULL >> >> ______________________________________________ >> 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. > >[[alternative HTML version deleted]]
Hi Paul, Perhaps # Data set set.seed(123) x=rnorm(100) y=x+2*rnorm(100) # ANOVA AOV=anova(lm (y ~ x)) p1=AOV$"Pr(>F)"[1] p1 or # ANOVA 2 AOV1=aov(y ~ x) p2=unlist(summary(AOV1))["Pr(>F)1"] p2 HTH, Jorge On Wed, May 7, 2008 at 8:47 PM, Paul Benton <hpbenton@scripps.edu> wrote:> hello all, > > Quick question, how do I get the p value out of the anova? > > Thanks, > > Paul > > > pb<-aov(as.numeric(diff[5,16:33]) ~ grF) > > summary(pb) > Df Sum Sq Mean Sq F value Pr(>F) > grF 3 2.7860e+10 9.2867e+09 4.2236 0.02534 * > Residuals 14 3.0783e+10 2.1988e+09 > --- > Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > > str(summary(pb)) > List of 1 > $ :Classes 'anova' and 'data.frame': 2 obs. of 5 variables: > ..$ Df : num [1:2] 3 14 > ..$ Sum Sq : num [1:2] 2.79e+10 3.08e+10 > ..$ Mean Sq: num [1:2] 9.29e+09 2.20e+09 > ..$ F value: num [1:2] 4.22 NA > ..$ Pr(>F) : num [1:2] 0.0253 NA > - attr(*, "class")= chr [1:2] "summary.aov" "listof" > > attr(summary(pb), "Pr(>F)") > NULL > > ______________________________________________ > 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.[[alternative HTML version deleted]]