Dear list, i am a biologist who needs to do some ttest between disease and non disease, sex, genotype and the serum levels of proteins on a large number of individuals. i have been using excel for a long time but it is very tedious and time consuming. i am posting the data below and ask your help in generating a code to get this analysis done in R. thanks gender disease genotype data M N CC 3.206447188 F N CC 8.2 M N CC 15.78908629 M N CC 21.14311843 F N CC 21.48413647 M N CC 30.08028842 M N CC 30.11455009 F N CC 32.41258845 F N CT 6622.253065 M N CT 6763.6 M N CT 7342.023209 F N CT 7617.7 F N CT 7857.3 M N CT 8027.78692 F N CT 8755.950438 M N CT 9007.7 F N CT 9157.76987 M N CT 9398.270953 F N CT 9710.083037 F N CT 9896.887277 M N CT 10082.60082 F N CT 10137.05244 F N CT 10350.76186 M N CT 14629.34508 F N TT 4.614829254 F N TT 5.223593964 F N TT 6.7 M N TT 6.7 M N TT 7.735287229 F N TT 13.68084134 F N TT 14.5 M N TT 15.3 M N TT 16.16826703 M N TT 19.8 M N TT 24.51271254 M N TT 29.92459383 F N TT 30.3993842 M N TT 30.57161207 F N TT 30.72031553 F N TT 31.8 F N TT 34.72409961 M N TT 37 F N TT 38.94507607 M N TT 39.1 M N TT 40.9 M N TT 41.5 F N TT 42.36614019 F Y CC 338.2166757 M Y CC 345.8711007 M Y CC 347.4659528 F Y CC 356.3 F Y CC 358.4 F Y CC 360.184259 F Y CC 453.8 F Y CC 573.7342373 M Y CC 962.1232959 F Y CC 1055.9 F Y CC 1309.532621 F Y CC 2798.6 F Y CC 3568.794326 M Y CT 1.227348206 F Y CT 2.061944986 F Y CT 2.245592643 M Y CT 2.454696412 M Y CT 2.456716738 M Y CT 4.318447391 M Y CT 4.503098245 M Y CT 5.873088452 M Y CT 7.106930564 F Y CT 7.7 M Y CT 10.83537709 M Y CT 11.4 M Y CT 12.1 M Y CT 12.62002743 M Y CT 13.6 F Y CT 13.7 F Y CT 14.35562171 F Y CT 15.9 F Y TT 986.6755719 F Y TT 1206.475083 F Y TT 1237.9 M Y TT 1254.5 F Y TT 1303.6 F Y TT 1573.915019 M Y TT 1756.8 M Y TT 1895 M Y TT 2126.766565 F Y TT 2149.512866 M Y TT 3249.449945 F Y TT 6999.3 M Y TT 7172.479241 M Y TT 8268.909251 M Y TT 8544.229671 -- View this message in context: http://www.nabble.com/ttest-in-R-tp22390889p22390889.html Sent from the R help mailing list archive at Nabble.com.
Hello friend. I believe anova might be a better solution for you. You might have a look here: http://www.personality-project.org/r/r.anova.html A simple R session that will work for you is: # getting the data in: data1 <- read.table( "enter the path of the file here, look at ?read.table for exact syntax) aov1 <- aov(data ~ gender + disease + genotype ,data = data1) summary(aov1) If you insist on t.test, here is the way: t.test(data ~ gender ,data = data1) t.test(data ~ disease ,data = data1) t.test(data ~ genotype ,data = data1) Cheers, Tal On Sat, Mar 7, 2009 at 9:23 PM, 1Rnwb <sbpurohit@gmail.com> wrote:> > Dear list, > > i am a biologist who needs to do some ttest between disease and non > disease, > sex, genotype and the serum levels of proteins on a large number of > individuals. i have been using excel for a long time but it is very tedious > and time consuming. i am posting the data below and ask your help in > generating a code to get this analysis done in R. thanks > > gender disease genotype data > M N CC 3.206447188 > F N CC 8.2 > M N CC 15.78908629 > M N CC 21.14311843 > F N CC 21.48413647 > M N CC 30.08028842 > M N CC 30.11455009 > F N CC 32.41258845 > F N CT 6622.253065 > M N CT 6763.6 > M N CT 7342.023209 > F N CT 7617.7 > F N CT 7857.3 > M N CT 8027.78692 > F N CT 8755.950438 > M N CT 9007.7 > F N CT 9157.76987 > M N CT 9398.270953 > F N CT 9710.083037 > F N CT 9896.887277 > M N CT 10082.60082 > F N CT 10137.05244 > F N CT 10350.76186 > M N CT 14629.34508 > F N TT 4.614829254 > F N TT 5.223593964 > F N TT 6.7 > M N TT 6.7 > M N TT 7.735287229 > F N TT 13.68084134 > F N TT 14.5 > M N TT 15.3 > M N TT 16.16826703 > M N TT 19.8 > M N TT 24.51271254 > M N TT 29.92459383 > F N TT 30.3993842 > M N TT 30.57161207 > F N TT 30.72031553 > F N TT 31.8 > F N TT 34.72409961 > M N TT 37 > F N TT 38.94507607 > M N TT 39.1 > M N TT 40.9 > M N TT 41.5 > F N TT 42.36614019 > F Y CC 338.2166757 > M Y CC 345.8711007 > M Y CC 347.4659528 > F Y CC 356.3 > F Y CC 358.4 > F Y CC 360.184259 > F Y CC 453.8 > F Y CC 573.7342373 > M Y CC 962.1232959 > F Y CC 1055.9 > F Y CC 1309.532621 > F Y CC 2798.6 > F Y CC 3568.794326 > M Y CT 1.227348206 > F Y CT 2.061944986 > F Y CT 2.245592643 > M Y CT 2.454696412 > M Y CT 2.456716738 > M Y CT 4.318447391 > M Y CT 4.503098245 > M Y CT 5.873088452 > M Y CT 7.106930564 > F Y CT 7.7 > M Y CT 10.83537709 > M Y CT 11.4 > M Y CT 12.1 > M Y CT 12.62002743 > M Y CT 13.6 > F Y CT 13.7 > F Y CT 14.35562171 > F Y CT 15.9 > F Y TT 986.6755719 > F Y TT 1206.475083 > F Y TT 1237.9 > M Y TT 1254.5 > F Y TT 1303.6 > F Y TT 1573.915019 > M Y TT 1756.8 > M Y TT 1895 > M Y TT 2126.766565 > F Y TT 2149.512866 > M Y TT 3249.449945 > F Y TT 6999.3 > M Y TT 7172.479241 > M Y TT 8268.909251 > M Y TT 8544.229671 > > -- > View this message in context: > http://www.nabble.com/ttest-in-R-tp22390889p22390889.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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. >-- ---------------------------------------------- My contact information: Tal Galili Phone number: 972-50-3373767 FaceBook: Tal Galili My Blogs: www.talgalili.com www.biostatistics.co.il [[alternative HTML version deleted]]
Thanks for the help, but ANOVA will give me a single pvalue, then how i can make sure which group is showing the significant differences. Tal Galili wrote:> > Hello friend. > > I believe anova might be a better solution for you. > You might have a look here: > http://www.personality-project.org/r/r.anova.html > > A simple R session that will work for you is: > > # getting the data in: > data1 <- read.table( "enter the path of the file here, look at > ?read.table > for exact syntax) > > aov1 <- aov(data ~ gender + disease + genotype ,data = data1) > summary(aov1) > > > If you insist on t.test, here is the way: > t.test(data ~ gender ,data = data1) > t.test(data ~ disease ,data = data1) > t.test(data ~ genotype ,data = data1) > > > Cheers, > Tal > > > > > On Sat, Mar 7, 2009 at 9:23 PM, 1Rnwb <sbpurohit at gmail.com> wrote: > >> >> Dear list, >> >> i am a biologist who needs to do some ttest between disease and non >> disease, >> sex, genotype and the serum levels of proteins on a large number of >> individuals. i have been using excel for a long time but it is very >> tedious >> and time consuming. i am posting the data below and ask your help in >> generating a code to get this analysis done in R. thanks >> >> gender disease genotype data >> M N CC 3.206447188 >> F N CC 8.2 >> M N CC 15.78908629 >> M N CC 21.14311843 >> F N CC 21.48413647 >> M N CC 30.08028842 >> M N CC 30.11455009 >> F N CC 32.41258845 >> F N CT 6622.253065 >> M N CT 6763.6 >> M N CT 7342.023209 >> F N CT 7617.7 >> F N CT 7857.3 >> M N CT 8027.78692 >> F N CT 8755.950438 >> M N CT 9007.7 >> F N CT 9157.76987 >> M N CT 9398.270953 >> F N CT 9710.083037 >> F N CT 9896.887277 >> M N CT 10082.60082 >> F N CT 10137.05244 >> F N CT 10350.76186 >> M N CT 14629.34508 >> F N TT 4.614829254 >> F N TT 5.223593964 >> F N TT 6.7 >> M N TT 6.7 >> M N TT 7.735287229 >> F N TT 13.68084134 >> F N TT 14.5 >> M N TT 15.3 >> M N TT 16.16826703 >> M N TT 19.8 >> M N TT 24.51271254 >> M N TT 29.92459383 >> F N TT 30.3993842 >> M N TT 30.57161207 >> F N TT 30.72031553 >> F N TT 31.8 >> F N TT 34.72409961 >> M N TT 37 >> F N TT 38.94507607 >> M N TT 39.1 >> M N TT 40.9 >> M N TT 41.5 >> F N TT 42.36614019 >> F Y CC 338.2166757 >> M Y CC 345.8711007 >> M Y CC 347.4659528 >> F Y CC 356.3 >> F Y CC 358.4 >> F Y CC 360.184259 >> F Y CC 453.8 >> F Y CC 573.7342373 >> M Y CC 962.1232959 >> F Y CC 1055.9 >> F Y CC 1309.532621 >> F Y CC 2798.6 >> F Y CC 3568.794326 >> M Y CT 1.227348206 >> F Y CT 2.061944986 >> F Y CT 2.245592643 >> M Y CT 2.454696412 >> M Y CT 2.456716738 >> M Y CT 4.318447391 >> M Y CT 4.503098245 >> M Y CT 5.873088452 >> M Y CT 7.106930564 >> F Y CT 7.7 >> M Y CT 10.83537709 >> M Y CT 11.4 >> M Y CT 12.1 >> M Y CT 12.62002743 >> M Y CT 13.6 >> F Y CT 13.7 >> F Y CT 14.35562171 >> F Y CT 15.9 >> F Y TT 986.6755719 >> F Y TT 1206.475083 >> F Y TT 1237.9 >> M Y TT 1254.5 >> F Y TT 1303.6 >> F Y TT 1573.915019 >> M Y TT 1756.8 >> M Y TT 1895 >> M Y TT 2126.766565 >> F Y TT 2149.512866 >> M Y TT 3249.449945 >> F Y TT 6999.3 >> M Y TT 7172.479241 >> M Y TT 8268.909251 >> M Y TT 8544.229671 >> >> -- >> View this message in context: >> http://www.nabble.com/ttest-in-R-tp22390889p22390889.html >> Sent from the R help mailing list archive at Nabble.com. >> >> ______________________________________________ >> R-help at 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. >> > > > > -- > ---------------------------------------------- > > > My contact information: > Tal Galili > Phone number: 972-50-3373767 > FaceBook: Tal Galili > My Blogs: > www.talgalili.com > www.biostatistics.co.il > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help at 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. > >-- View this message in context: http://www.nabble.com/ttest-in-R-tp22390889p22400624.html Sent from the R help mailing list archive at Nabble.com.