Dear all, How can I retrieve only p-value to store it in a file after applying anova() on some microarray gene expression data set?? For example, *Suppose my result is:* * * *Analysis of Variance Table* * * *Response: wt* * Df Sum Sq Mean Sq F value Pr(>F) * *treat 1 1.2100 1.2100 5.548 0.03361 ** *Residuals 14 3.0534 0.2181 * *---* *Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 * I want to store only p-value(0.03361) in a file. Thanks in advance, Anirban [[alternative HTML version deleted]]

This has nothing to do with Bioconductor and would be fruitfully posed on R-help -- if the answer were not findable otherwise. In this case, a reproducible example is example(lm) names(anova(lm.D9)) anova(lm.D9)["group","Pr(>F)"] to store the number to a file requires other facilties, see ?write.table or the like On Sat, Sep 10, 2011 at 10:26 PM, ANIRBAN BHAR <aec.ani@gmail.com> wrote: > Dear all, > > How can I retrieve only p-value to store it in a file after applying > anova() > on some microarray gene expression data set?? > > For example, > > *Suppose my result is:* > * > * > *Analysis of Variance Table* > * > * > *Response: wt* > * Df Sum Sq Mean Sq F value Pr(>F) * > *treat 1 1.2100 1.2100 5.548 0.03361 ** > *Residuals 14 3.0534 0.2181 * > *---* > *Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 * > > I want to store only p-value(0.03361) in a file. > > Thanks in advance, > > Anirban > > [[alternative HTML version deleted]] > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

summary(anovaObject)[[1]]["treat", "Pr(>F)"]

Hi, When in doubt, use the function `str` on a variable to see its structure: > a <- anova(lm(y ~ x)) > str(a) Classes 'anova' and 'data.frame': 2 obs. of 5 variables: $ Df : int 1 8 $ Sum Sq : num 6.89 6.29 $ Mean Sq: num 6.886 0.787 $ F value: num 8.75 NA $ Pr(>F) : num 0.0182 NA - attr(*, "heading")= chr "Analysis of Variance Table\n" "Response: y" Of this we can see, that the P-values are accessible via: > a$"Pr(>F)" There might be some built-in accessor-function but that is up to the reader. `str` is useable on almost any variable, although in some cases it might flood your console when used on a larger, more complex object. Kind regards, Stefan McKinnon H?j-Edwards Dept. of Genetics and Biotechnology PhD student Faculty of Agricultural Sciences stefan.hoj-edwards at agrsci.dk Aarhus University Tel.: +45 8999 1291 Blichers All? 20, Postboks 50 Web: www.iysik.com DK-8830?Tjele Tel.: +45 8999 1900 Web: www.agrsci.au.dk ------------------------------ Message: 2 Date: Sun, 11 Sep 2011 04:26:19 +0200 From: ANIRBAN BHAR <aec.ani@gmail.com> To: bioconductor at r-project.org Subject: [BioC] Problem to store p-value of anova() method Message-ID: <cac1mboukf4ic8pnylhmedq4q5dt0z17mvvh+vmitiph56z68vq at="" mail.gmail.com=""> Content-Type: text/plain Dear all, How can I retrieve only p-value to store it in a file after applying anova() on some microarray gene expression data set?? For example, *Suppose my result is:* * * *Analysis of Variance Table* * * *Response: wt* * Df Sum Sq Mean Sq F value Pr(>F) * *treat 1 1.2100 1.2100 5.548 0.03361 ** *Residuals 14 3.0534 0.2181 * *---* *Signif. codes: 0 ?***? 0.001 ?**? 0.01 ?*? 0.05 ?.? 0.1 ? ? 1 * I want to store only p-value(0.03361) in a file. Thanks in advance, Anirban