I have 15 genotypes each of corn and sorghum, planted in 2 different irrigation regimes with 3 replications in each regimes. I have data related to these 6 replications - yield/area, yield/panicle, chlorophyll content, plant height, total plant weight, harvest index, etc. I need to estimate BLUEs, BLUPs, prediction and/or estimate table of effect of each line for a major trait and effect of each environment for the same trait using mixed model (also Bayesian but not REML because some variance components are in negative values) in JMP.
You should submit your analysis to JMP desk but yur variables are discrete as far species and possibly irrigation at 2 levels and a preliminar step in 2 way ANOVA can indicate if the random error is quite high for multilinear models
Rahul this will depend on the model you are building. Is this a split plot design? When you build the model to estimate BLUES you are treating genotypes as fixed to estimate the BLUES and another model treating genotypes as random to estimates BLUPS. The reason you are getting negative variances is not because of REML it is because you have left the "unbounded variance components" this is useful in some cases. But I would recommend running REML. If they are negative and you leave them bounded they will be estimated as zero. Hope this helps.
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