[R] HELP relevel INTERCEPT-COMPARISONS

[CHIRIBOGA Xavier]

Dear colleagues,


How can I do to "relevel" the intercept?

I need that the treatment "Db" be the intercept, and have p-values for the comparisons with the others treatments.

I used the function "relevel" but it did not work out to have what I want.

Thanks for your help,


Xavier


T1 <- read.table(file.choose(), h=T)
> head(T1)
  treatment replicate Time     Ebcg
1   CHA0+Db         1    1  9681172
2   CHA0+Db         2    1  5599000
3   CHA0+Db         3    1 10280480
4   CHA0+Db         4    1  1004526
5   CHA0+Db         5    1 12942018
6   CHA0+Db         6    1  7478773
> attach(T1)
> summary(T1)
   treatment   replicate          Time        Ebcg
 CHA0   :6   Min.   :1.000   Min.   :1   Min.   :       0
 CHA0+Db:9   1st Qu.:2.750   1st Qu.:1   1st Qu.: 1000922
 Db     :9   Median :4.500   Median :1   Median : 4044094
 Healthy:9   Mean   :4.625   Mean   :1   Mean   : 5699717
 PCL    :6   3rd Qu.:6.250   3rd Qu.:1   3rd Qu.: 7785782
 PCL+Db :9   Max.   :9.000   Max.   :1   Max.   :24736254
> hist(Ebcg)
> treatment<-relevel(treatment,ref="Db")
> mT1<-lm(sqrt(Ebcg)~treatment,data=T1)
> summary(mT1)

Call:
lm(formula = sqrt(Ebcg) ~ treatment, data = T1)

Residuals:
     Min       1Q   Median       3Q      Max
-1748.12  -540.19     0.97   545.14  1949.22

Coefficients:
                                 Estimate         Std. Error     t value     Pr(>|t|)
(Intercept)                     532.5          384.4       1.385         0.173296
treatmentCHA0+Db   2048.5          496.3       4.128         0.000170 ***
treatmentDb                2491.9          496.3       5.021         9.93e-06 ***
treatmentHealthy       1215.6          496.3       2.450         0.018552 *
treatmentPCL                120.4          543.6       0.221         0.825816
treatmentPCL+Db        2098.9          496.3       4.229         0.000124 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 941.6 on 42 degrees of freedom
Multiple R-squared:  0.5206,    Adjusted R-squared:  0.4635
F-statistic: 9.121 on 5 and 42 DF,  p-value: 6.227e-06



Xavier Chiriboga M.
PhD Candidate
Fundamental and Applied Research in Chemical Ecology Lab.
Institute of Biology
University of Neuchatel

Website: https://www.unine.ch/farce/home/membres/xavier-chiriboga.html

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