Hi !

I am running an interaction lmer model to check the interaction significance for a response variable (height) vs KASP markers (M1, M2, M3) ---- as an example. Here is the model:

modelz <- lmer(Julian.Days ~ VRN * PPD1 * PPD2 + (1|REP), data = inputData)

When I run the 'anova' command on this model this is the message I get:

Missing cells for: VRNXX:PPD1XX, VRNXX:PPD1XY, VRNXX:PPD2YY, PPD1XX:PPD2YY.... (other interaction combinations). Interpret Type III hypothesis with care

I don't really understand what this message is saying... I don't have any missing data in my csv file. Each marker category has at least 2 types of marker calls XX/YY.

As a result my anova output looks like this:

           Sum Sq Mean Sq NumDF DenDF F value    Pr(>F)    
VRN            37.302  37.302     1   187  4.2278   0.04116 *  
PPD1          264.937 132.469     2   187 15.0139 8.974e-07 ***
PPD2           57.538  57.538     1   187  6.5214   0.01146 *  
VRN:PPD1                                                       
VRN:PPD2 
VRN:PPD2                                                       
PPD1:PPD2                                                      
 VRN:PPD1:PPD2
  

VRN:PPD1:PPD2

  Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
  

Can someone please help me understand what is going on??

Thanks in advance!