diff --git a/assays/StatisticalAnalysis/protocols/FieldExperiment.md b/assays/StatisticalAnalysis/protocols/FieldExperiment.md index 3ae341617d2572caacb8de81c5db90c02749dbe1..95d8de18661b3bb01f082cee48bc866bc9827420 100644 --- a/assays/StatisticalAnalysis/protocols/FieldExperiment.md +++ b/assays/StatisticalAnalysis/protocols/FieldExperiment.md @@ -7,13 +7,13 @@ $$y_{(p)ijklmnopqr} = \mu + G_i + E_j + (G:E)_{ij} + ZS_k + L_l + S_m + (G:L)_{i where $y_{(p)ijklmnopqr}$ was the observed MultispeQ parameter across all light conditions and all developmental stages, μ the general mean, $G_i$ the effect of the *i*th inbred, $E_j$ the effect of the *j*th environment, $(G:E)_{ij}$ the interaction between the *i*th inbred and the *j*th environment, $ZS_k$ the effect of the *k*th Zadoks score of barley development, $L_l$ the effect of the *l*th light intensity cluster, $S_m$ the effect of the *m*th barely developmental phase, $(G:L)_{il}$ the interaction between the *i*th inbred and the *l*th light intensity cluster, $(G:S)_{im}$ the interaction between the *i*th inbred and the *m*th barley developmental phase, $M_n$ the effect of the *n*th MultispeQ device, $D_o$ the effect of measurement date, $(E:R)_{jp}$ the effect of the *p*th replicate nested within the *j*th environment, $(E:R:B)_{jpq}$ the effect of the *q*th block nested within the *p*th replicate in the *j*th environment, $PAR_{ijklmnor}$ the light intensity of each measurement, $T_{ijklmnor}$ the ambient temperature of each measurement, and $\epsilon_{(p)ijklmnopqr}$ the random error. -To estimate adjusted entry means for MultispeQ parameters of all inbreds, $G_i, E_j, (G:E)_{ij}, ZS_k, L_l, S_m, (G:L)_{il}, and (G:S)_{im}$ were treated as fixed effects, and $M_n, D_o, (E:R)_{jp}, (E:R:B)_{jpq}$ as random effects, $PAR_{ijklmnor} and T_{ijklmnor}$ were covariates. Furthermore, we calculated adjusted entry means for all inbreds for each light intensity cluster as well as each developmental phase. +To estimate adjusted entry means for MultispeQ parameters of all inbreds, $G_i, E_j, (G:E)_{ij}, ZS_k, L_l, S_m, (G:L)_{il}, and (G:S)_{im}$ were treated as fixed effects, and $M_n, D_o, (E:R)_{jp}, (E:R:B)_{jpq}$ as random effects, $PAR_{ijklmnor}$ and $T_{ijklmnor}$ were covariates. Furthermore, we calculated adjusted entry means for all inbreds for each light intensity cluster as well as each developmental phase. In addition, to evaluate the effect of each fixed factor and covariate, analysis of variance (ANOVA) was conducted. To assess the heritability of each photosynthesis-related parameter at each developmental stage, which was considerably shorter than the above-mentioned three developmental phases, data were separated into eight stages from Zadoks principal growth stages. The adjusted entry means were calculated based on the following model: -*(6)* +**(6)** $$y_{(pd)ijlnopqr} = \mu + G_i + E_j + M_n + D_o + PAR_{ijklmnor} + T_{ijklmnor} + (E:R)_{jp} + (E:R:B)_{jpq} + \epsilon_{(p)ijklmnopqr}$$ where, $y_{(pd)ijlnopqr}$ was the photosynthesis-related parameter for each developmental stage across all other factors. Due to convergence problems, the interaction between $G_i and E_j$ was removed from this model.