Dear Phil,   Thank you so much, I am not perfect in statistic and SEM, I am just a beginner. Your advice was useful to me. Your link that you sent me was helpful. I ran SEM without residuals because I am not sure if I can use them in the model based on my purpose. I think that I need to learn more about residuals. Of course, I found some papers that they used the residuals in the model.   I learnt more things from your advice.  Thank you so much for your time,   Sincerely yours, Milad ... View more

Dear Phil, Thank you for your message.    I mean the residuals that I saved them from the model that I ran by "Genotype" and "Block" randomly.  I believe that I should work more on it until I use them.  I want to run a sem with R, I just want to calculate and prepare data in JMP.    Thank you so much, Milad     ... View more

Dear Mark,   Thank you so much for your advice,  I searched about " Prediction Profiler ". It looks good. I believe that it would be helpful.   Thank you, Best regards, Milad ... View more

Dear Phil,   Thank you so much for your time, it was great.  Yes, the effect of "Genotype" is not important for me. I want to remove it from my data. I think maybe I can evaluate variables in a better condition. I think your solution is great. Do you think that I can use these residuals as new variables to reduce the "Genotype" effect? Because I want to use them in the structural equation model.   Best regards, Milad   ... View more

Dear Phil, Thank you so much for your time to advise me.    I have attached the factors with a part of my data. Please find it. I couldn't attach the .jmp file, I saw this message: " The contents of the attachment doesn't match its file type. ". So I put the image of steps and attached the excel sheet. This experiment is factorial under RCBD. Genotype (4 levels, A, B, C, and D), Nutrient 1 (2 levels, 10 and 40), and Nutrient 2 (2 levels, 25 and 100) are factors in 4 blocks. Also, "Variable 1" and "Variable 2" are variables that I measured during the experiment period. In this file, I transformed the variables in logarithm.  For example, different "Genotype"s had a different effect on "Variable 2". While I just need the effects of "Nutrient 1" and "Nutrient 2" in the model. So, I want to remove the effect of "Genotype" from "Variable 1" and "Variable 2". For this purpose, first I used "Fit Y by X" for each variable by "Genotype", then I saved the residuals for each variable.   Step 1. Fit y by x.  In the second step, I used these residuals in "Fit model" by "Block, Nutrient 1, Nutrient 2, Nutrient 1*Nutrient 2" as full factorial. After that, I saved the residuals that I obtained from this method and used them as new variables. I mentioned, "Step 1" and "Step 2" in "Data table" in this file. Also, "Step () - Variable ()" are residuals that I saved from each step for each variable. (I couldn't attach .jmp file). For these variables, I just removed two outliers that you can see them in this file (row 20 and 61).    Step 2. As a result when I used this method, regression between some of the variables is different. For example, regression between two variables would be changed to positive from negative.    Thank you so much, Sincerely yours, Milad ... View more

Dear Phil, Thank you so much for your time and clear explanation.    I saw the links that you mentioned. I think the effects of A*B and A*C and B*C on variables in my experiment look like to design 2, so they are not orthogonal.  Could you please check out the process that I did to remove the effect of A from my variables? 1. I saved the residuals from A with each variable.  2. I run full factorial (B and C) on saved residuals. Then I saved the residuals as a new variable.  Now, the effect of A has been removed from the new variables.  Do you think it is correct?   Thank you so much for your time,  Cheers, Milad   ... View more

Dear @markbailey Thank you so much.  It was great,   Cheers, Milad ... View more

Dear @Peter_Bartell Thank you so much for your time and your suggestion. It is realy useful.    ... View more

Dear @markbailey Thank you so much for your time and your explanation. I mean that I report the ANOVA results and I report the mean comparison based on original data. For example, I have a series of data in form of percentage. They were not normal and I transformed them by log and analyze them. Now, for mean comparison, should I use the data based on unnormalized or normalized data?     ... View more