Dear colleagues,
I am analyzing a data set of 68 values (integers). In some treatments (exactly 6) the values are "zero". Because I record 0 in my measurement (or really a small value below zero) My experiment is designed in such a way that I record values for 6 treatments at 2 times. Replicates are different in each combination time-treatment. I am running a GLM , poisson distribution, for ANOVA I used Chisq, and for the POST HOC test I used Tukey. I try to detect if interaction is significant, so I build the script: expresion~time*treatment Effects of time, treatment are interaction are significant. However, when I run the script for Tukey comparisons, I only get 15 comparisons. Of course I cannot interpret that: these comparisons are the same for Time 1 and Time 2, since there is a significant effect of time. Moreover, I got a warning message : covariate interactions found. I dont know if I am doing right? I dont know what to do? Thank you for your help, Xavier PhD Student University of Neuchatel lm3=glm(expresion~time*treatment,family="poisson") > summary(lm3) Call: glm(formula = expresion ~ time * treatment, family = "poisson") Deviance Residuals: Min 1Q Median 3Q Max -5.3796 -1.4523 -0.6642 1.2277 6.3909 Coefficients: Estimate Std. Error z value Pr(>|z|) (Intercept) 2.09964 0.29508 7.115 1.12e-12 *** time 0.20294 0.19255 1.054 0.291895 treatmentCHA0+Db -0.17004 0.36180 -0.470 0.638356 treatmentDb 1.68952 0.37624 4.490 7.11e-06 *** treatmentHEALTHY 0.84035 0.50340 1.669 0.095049 . treatmentPCL 0.32072 0.37950 0.845 0.398041 treatmentPCL+Db 0.54365 0.34047 1.597 0.110320 time:treatmentCHA0+Db 0.87314 0.22626 3.859 0.000114 *** time:treatmentDb -0.82803 0.26539 -3.120 0.001808 ** time:treatmentHEALTHY -1.36987 0.38318 -3.575 0.000350 *** time:treatmentPCL 0.08474 0.24635 0.344 0.730851 time:treatmentPCL+Db 0.39244 0.21521 1.824 0.068217 . --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Dispersion parameter for poisson family taken to be 1) Null deviance: 1173.05 on 66 degrees of freedom Residual deviance: 403.07 on 55 degrees of freedom AIC: 707.95 Number of Fisher Scoring iterations: 5 > anova(lm3,test="Chisq") Analysis of Deviance Table Model: poisson, link: log Response: expresion Terms added sequentially (first to last) Df Deviance Resid. Df Resid. Dev Pr(>Chi) NULL 66 1173.05 time 1 100.55 65 1072.50 < 2.2e-16 *** treatment 5 561.69 60 510.81 < 2.2e-16 *** time:treatment 5 107.75 55 403.07 < 2.2e-16 *** --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 > summary(glht(lm3, mcp(treatment="Tukey"))) Simultaneous Tests for General Linear Hypotheses Multiple Comparisons of Means: Tukey Contrasts Fit: glm(formula = expresion ~ time * treatment, family = "poisson") Linear Hypotheses: Estimate Std. Error z value Pr(>|z|) CHA0+Db - CHA0 == 0 -0.1700 0.3618 -0.470 0.9970 Db - CHA0 == 0 1.6895 0.3762 4.490 <0.001 *** HEALTHY - CHA0 == 0 0.8404 0.5034 1.669 0.5402 PCL - CHA0 == 0 0.3207 0.3795 0.845 0.9568 PCL+Db - CHA0 == 0 0.5437 0.3405 1.597 0.5892 Db - CHA0+Db == 0 1.8596 0.3135 5.931 <0.001 *** HEALTHY - CHA0+Db == 0 1.0104 0.4584 2.204 0.2266 PCL - CHA0+Db == 0 0.4908 0.3174 1.546 0.6231 PCL+Db - CHA0+Db == 0 0.7137 0.2696 2.648 0.0817 . HEALTHY - Db == 0 -0.8492 0.4699 -1.807 0.4491 PCL - Db == 0 -1.3688 0.3338 -4.101 <0.001 *** PCL+Db - Db == 0 -1.1459 0.2887 -3.969 <0.001 *** PCL - HEALTHY == 0 -0.5196 0.4725 -1.100 0.8764 PCL+Db - HEALTHY == 0 -0.2967 0.4418 -0.672 0.9842 PCL+Db - PCL == 0 0.2229 0.2929 0.761 0.9725 --- Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 (Adjusted p values reported -- single-step method) Warning message: In mcp2matrix(model, linfct = linfct) : covariate interactions found -- default contrast might be inappropriate [[alternative HTML version deleted]] ______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see 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.