CODEWITHSUNDEEP
glmp-valuetukey
Annalese Jane
Annalese Jane

Reputation: 51

Extracting raw p-values from glm glht function (instead of Tukey adjusted p-values)

I was given the code below and asked to extract the raw p-values rather than the Tukey adjusted values (as we will be adjusting for multiple comparisons using Homes-Bonferroni at a later stage), but I'm not sure what to replace "Tukey" with (I'm new to using R).....

        res=glht(x, linfct=mcp(Letter="Tukey")
        out=summary(res)
        out

Upvotes: 1

Views: 2001

Answers (1)

Annalese Jane
Annalese Jane

Reputation: 51

I found the answer. For anyone else who is interested... The "Tukey" option for the glht function in the multcomp package does not actually use the Tukey correction, it just sets up all pairwise comparisons. It doesn't do p-values; for that you need summary.glht. To get the raw p values you use test=adjusted("none").

res=glht(x, linfct=mcp(Letter="Tukey")
   out=summary(res, test = adjusted("none"))
   out

Upvotes: 4

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