I tried to plot the data and did not see a trend of increasing total sporangia with increasing number of root tips. I guess I can not say confidently that sporangia production is not affected by the total number of root tips of an individual plant, as you mentioned, there are only 3 obervations for each isolate.    So If I use the number of root tips of each plant as covariate in a model, and if it does not have significant effect in the model (P>0.5), can I draw the conclusion that the number of root tips of each plant does not affect sporangia production?    For the test above (set the number of root tips of each plant as a covariate), I think I have to use the total number of sporangia of each plant, if the test result is not significant, can I jump to analyzing the data using number of sporangia on each root tip?   Also, I was wondering how can I test if there is a significant difference of sporangia production by the same isolate across different runs?   Sorry for keeping bugging you...I really appreciate your help! ... View more

Yes, I absolutely agree you on the two possibilities. And based on my observation, I tend to believe possibility 1 was what happened.    I was wondering how to test if this concern has a significant effect on sporangia production?    I guess if I use the total number of sporangia produced by each plant for analysis, I can use the number of root tips of each plant as a covariate in the model. But what if I wanna use the  number of sporangia per root tip, could you give me some advice on how to test the potential concern in SAS program? Honestly, I have no idea how to test it in SAS.   Thank you! ... View more

Thank you for your kind reply and I really appreciated your help so far!   I guess it will be helpful to provide you more details about how I did this experiment. So I used 10ml of 10^4 zoospores/ml zoospore suspension to infect each plant (the zoospore suspensions were generated by the 2 fungal isolates that I was trying to compare their sporangia production ability around plant root tips after infection, the zoospore suspensions were adjusted to same concentration). And I left the whole root system of an individual plant in that 10ml of 10^4 zoospores/ml zoospore suspension for infection.    My concern is that since the number of root tips of each plant is different, if a plant had a higher number of root tips, on average, each root tip was facing fewer number of zoospores during the infection process compared to a plant that had fewer root tips (So root tips from the same plant were facing same number of zoospores during infection but root tips from different plants were not facing the same number of zoospores). I am worried about if that will be a factor affecting the final number of sporangia growing around root tips from different plants. Hope I made it clear this time.   Again, thanks for your kind attention!    ... View more

Hi sld,   Sorry for keeping bugging you two month later since my initials post.   I just had another question about my data analysis. Since the number of root tips was different in each plant, so basically the sample sizes were different for each isolate by run combination (and I am also thinking the root tips sampled from an individual plant may share more similarity than root tips sampled from different plants), I was wondering how to test if the number of root tips in an individual plant has an effect on the dependent variable (sporangia) and how to test if different plants have an effect on the dependent variable?   Hope to hear your advice. Thank you in advance!   ... View more

Hi sld, thank you so much for your kind reply! ... View more

Thanks, Rick! ... View more

Hi sld, thanks for your kind reply! Yes, I was asking about estimates of lsmeans. I just had another question, if the default link function for "negbin" is "log", does specifying negative binomial distribution for counting data equal to log transformation?  ... View more

Hi sld,   Sorry for keep bugging you. But I had this question for a while and I haven't been able to figure it out myself.    I was wondering why specifying negative binomial of the counting data would give negative estimates? Hope you could give me some hints. I will really appreciate it!    Thanks in advance!  ... View more

Thank you so much!  ... View more

Hi PaigeMiller,   Sorry to keep bugging you. I just came across this question when I was trying to do the analysis using the actual number of days instead of the disease severity values assigned.    The experiment was done in a 28-day period, some of the plants did not show any symptoms at day 28. Theoretically, the number of days for those plants did not show any symptoms (healthy plants) will be infinite. I was wondering how should I deal with this kind of situation? Hope you could give me some tips.    Thank you! ... View more

Thank you so much for the suggestions and the correction of the SAS code!   I actually have the actual number of days recorded, I can definitely try that for the analysis.    Thanks again! I really appreciated your great help!  ... View more

Oh.. sorry about the Excel files. Since the dependent variable only takes 10, 8, 6, 4, 2, 0, I considered it as categriocal. I guess this is a really naive question, can I take the dependent variable as numeric although the value is not continuously assigned? The following the data set and the sas code I tried, just added rep as a random effect. Really appreciated your help!     data severity; input isolate $ rep disease; datalines; R0-G5-6 1 8 R0-G5-6 2 10 R0-G5-6 3 6 R0-G5-6 4 8 R0-G5-6 5 8 R0-G5-6 6 6 R0-G5-6 7 6 R0-G5-6 8 6 R0-G5-6 9 6 R0-G5-6 10 8 R0-G5-6A 1 0 R0-G5-6A 2 0 R0-G5-6A 3 0 R0-G5-6A 4 0 R0-G5-6A 5 0 R0-G5-6A 6 10 R0-G5-6A 7 0 R0-G5-6A 8 0 R0-G5-6A 9 0 R0-G5-6A 10 0 R0-G5-6B 1 8 R0-G5-6B 2 8 R0-G5-6B 3 8 R0-G5-6B 4 8 R0-G5-6B 5 8 R0-G5-6B 6 10 R0-G5-6B 7 6 R0-G5-6B 8 8 R0-G5-6B 9 8 R0-G5-6B 10 8 R0-G5-6C 1 10 R0-G5-6C 2 10 R0-G5-6C 3 8 R0-G5-6C 4 8 R0-G5-6C 5 8 R0-G5-6C 6 10 R0-G5-6C 7 6 R0-G5-6C 8 8 R0-G5-6C 9 8 R0-G5-6C 10 6 R0-G5-6E 1 6 R0-G5-6E 2 6 R0-G5-6E 3 4 R0-G5-6E 4 6 R0-G5-6E 5 6 R0-G5-6E 6 8 R0-G5-6E 7 6 R0-G5-6E 8 6 R0-G5-6E 9 8 R0-G5-6E 10 8 R0-G5-6F 1 4 R0-G5-6F 2 6 R0-G5-6F 3 6 R0-G5-6F 4 6 R0-G5-6F 5 8 R0-G5-6F 6 8 R0-G5-6F 7 8 R0-G5-6F 8 6 R0-G5-6F 9 8 R0-G5-6F 10 6 R0-G5-6G 1 6 R0-G5-6G 2 4 R0-G5-6G 3 6 R0-G5-6G 4 8 R0-G5-6G 5 6 R0-G5-6G 6 8 R0-G5-6G 7 8 R0-G5-6G 8 10 R0-G5-6G 9 2 R0-G5-6G 10 0 R0-G5-6H 1 10 R0-G5-6H 2 10 R0-G5-6H 3 4 R0-G5-6H 4 10 R0-G5-6H 5 6 R0-G5-6H 6 6 R0-G5-6H 7 8 R0-G5-6H 8 6 R0-G5-6H 9 10 R0-G5-6H 10 8 R0-G5-6I 1 6 R0-G5-6I 2 6 R0-G5-6I 3 8 R0-G5-6I 4 6 R0-G5-6I 5 6 R0-G5-6I 6 8 R0-G5-6I 7 8 R0-G5-6I 8 6 R0-G5-6I 9 8 R0-G5-6I 10 6 R0-G5-6J 1 8 R0-G5-6J 2 8 R0-G5-6J 3 8 R0-G5-6J 4 8 R0-G5-6J 5 8 R0-G5-6J 6 6 R0-G5-6J 7 6 R0-G5-6J 8 6 R0-G5-6J 9 8 R0-G5-6J 10 6 R0-G2-6 1 8 R0-G2-6 2 8 R0-G2-6 3 6 R0-G2-6 4 8 R0-G2-6 5 6 R0-G2-6 6 4 R0-G2-6 7 8 R0-G2-6 8 8 R0-G2-6 9 2 R0-G2-6 10 6 R0-G2-6A 1 6 R0-G2-6A 2 8 R0-G2-6A 3 8 R0-G2-6A 4 6 R0-G2-6A 5 8 R0-G2-6A 6 0 R0-G2-6A 7 8 R0-G2-6A 8 0 R0-G2-6A 9 0 R0-G2-6A 10 0 R0-G2-6B 1 6 R0-G2-6B 2 0 R0-G2-6B 3 0 R0-G2-6B 4 8 R0-G2-6B 5 6 R0-G2-6B 6 4 R0-G2-6B 7 4 R0-G2-6B 8 2 R0-G2-6B 9 6 R0-G2-6B 10 8 R0-G2-6C 1 8 R0-G2-6C 2 8 R0-G2-6C 3 8 R0-G2-6C 4 0 R0-G2-6C 5 0 R0-G2-6C 6 8 R0-G2-6C 7 0 R0-G2-6C 8 6 R0-G2-6C 9 6 R0-G2-6C 10 4 R0-G2-6D 1 2 R0-G2-6D 2 6 R0-G2-6D 3 4 R0-G2-6D 4 0 R0-G2-6D 5 2 R0-G2-6D 6 8 R0-G2-6D 7 0 R0-G2-6D 8 6 R0-G2-6D 9 6 R0-G2-6D 10 0 R0-G2-6E 1 0 R0-G2-6E 2 0 R0-G2-6E 3 8 R0-G2-6E 4 6 R0-G2-6E 5 6 R0-G2-6E 6 2 R0-G2-6E 7 8 R0-G2-6E 8 8 R0-G2-6E 9 4 R0-G2-6E 10 6 R0-G2-6F 1 2 R0-G2-6F 2 0 R0-G2-6F 3 8 R0-G2-6F 4 6 R0-G2-6F 5 6 R0-G2-6F 6 8 R0-G2-6F 7 6 R0-G2-6F 8 6 R0-G2-6F 9 8 R0-G2-6F 10 8 R0-G2-6G 1 0 R0-G2-6G 2 6 R0-G2-6G 3 0 R0-G2-6G 4 6 R0-G2-6G 5 2 R0-G2-6G 6 8 R0-G2-6G 7 6 R0-G2-6G 8 6 R0-G2-6G 9 6 R0-G2-6G 10 8 R0-G2-6H 1 6 R0-G2-6H 2 4 R0-G2-6H 3 8 R0-G2-6H 4 6 R0-G2-6H 5 2 R0-G2-6H 6 0 R0-G2-6H 7 8 R0-G2-6H 8 8 R0-G2-6H 9 8 R0-G2-6H 10 6 R0-G2-6I 1 4 R0-G2-6I 2 0 R0-G2-6I 3 0 R0-G2-6I 4 6 R0-G2-6I 5 6 R0-G2-6I 6 2 R0-G2-6I 7 6 R0-G2-6I 8 4 R0-G2-6I 9 8 R0-G2-6I 10 0 R0-G2-6J 1 6 R0-G2-6J 2 4 R0-G2-6J 3 6 R0-G2-6J 4 6 R0-G2-6J 5 6 R0-G2-6J 6 2 R0-G2-6J 7 6 R0-G2-6J 8 0 R0-G2-6J 9 2 R0-G2-6J 10 8 ; proc print data=severity; proc glimmix data=severity; class isolate rep; model disease=isolate; random rep; lsmeans isolate/ lines; run;   ... View more

Thanks for your suggestion!   Yes, in my case, Y which has values of 10,8,6,4,2,0, repsents the disease severity caused by a pathogen. X is the different pathogenic isolates, which is also categorical. What I am trying to do is to compare the disease severity caused by different pathogenic isolates on the same host.    I'll take a look at Proc catmod and try it out, thanks again! ... View more

Hi PaigeMiller,   Thanks for your kind reply!   My experiment was to compare the disease severity caused by 21 pathogenic isolates on the same host plant. 10 host plants were used as replicates for each single isolate inoculation. So there were 21*10=210 plants used in total. And disease severity was assigned accroding to when the plants showed disease symptoms: 1-6 days=10, 7-10 days=8, 11-16 days=6, 17-22 days=4, 23-28 days=2, and no symptoms at day 28=0. I've attached the data set here, if you would like to take a look at it. I'd like to use PROC GLIMIXX, but I am not sure how to specify that the response is categorical in the SAS code. Hope you could give me more suggestions. Thanks in advance!  ... View more