Please see attachement
all the “a-f” and “x1-x12” are variables.
Objective 1 : to compare methylation difference in CpG1 within group 1 between two time points 1 and 2, WITHOUT adjusting for cell count ( lymp,mo, gr).
Objective 2 : to compare methylation difference in CpG1 within group 2 between two time points 1 and 2, WITHOUT adjusting for cell count (lymp,mo and gr)
I have already analysed the comparison between group 1 pre and post and observed no significant difference in methylation in this group.
However in group 2 I have observed significant difference in the methylation between the two time point pre (T1) and post (T2).
Objective 3 : to compare methylation difference in CpG1 within group 1 between two time points 1 and 2, WITH adjusting for cell count ( lymp,mo, gr).
Objective 24: to compare methylation difference in CpG1 within group 2 between two time points 1 and 2, WITH adjusting for cell count (lymp,mo and gr)
From literature we know that blood counts also contribute significantly to methylation. I would like to adjust/correct for this information before comparing the two time points within the groups
After referring several websites i know i can do the lmer analysis, keeping time as random variable. i.e. Fit a varying intercept model with lmer
myexample
Usually I use SAS and the PROC MIXED module to carry out mixed models analyses. It is not easy for me to correctly interpret your R-code. But I wonder if you have included an interaction effect between group and time usually we want to take a difference in progress across groups into consideration. I also wonder if you have set the covariance structure and I think that UN, unstructured could be a good choice here.
You also need to if you have equal variances across grouping variables and co-variates. An other thing you need to check the normal assumption of the residuals.
Kind regards
Magnus Backheden
Dear Cristian,
I will definitely look through the models you suggested and also go through the link. Will keep in touch once I execute these.
regards
smeeta
- Badges
- Science topic
- Similar topics
- Mathematical Sciences
- Statistics
- Statistical Software
- SPSS