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Dependence of such measures on window sizes is common. You, however, have additional problems for this analysis. there is in general more methylation in the mutant samples than non-mutant, and this i …

The area under the receiver operating characteristic curve (AUROC) for each year is a good start at validation, but that doesn't provide information about the calibration of your model: how closely pr …

For a binary outcome, as in your example of whether a cell has a proliferation score greater than 0.5, you should use a binomial regression; logistic regression is a common choice. For that you provid …

First, look at the data. I saved your sample data in a data frame CD45 and looked at boxplots: CD45$sample <- as.factor(CD45$sample) # that avoids problems with using numeric values for sample labels …

That you only have 2 different types of oil doesn't prevent you from performing a Tukey HSD test. That's a test on all pairwise comparisons of means. You have 5 different combinations of those oils in …

Yes, correction for multiple hypothesis testing is important, but you have to consider it in the context of how these types of biomedical investigations can (and should) proceed. One important issue i …

It's difficult (impossible?) to calculate the a-priori power of a mixed model with formulas. The best approach is to simulate not only your data but also your sampling from the data. Simulate a very l …

I've heard that scientific journals "don't like" when researchers use planned comparison, so getting published with planned comparisons would be difficult if not near impossible. I haven't heard tha …

For the situation you describe you don't need to consider a multilevel model. Each dish only sees a single drug treatment so there is no way to distinguish whether cells are small because of the dish; …

Your question could be dealt with as a type of variable-selection or feature-selection problem. This is a very broad issue, as you can tell by following that tag on this site. With only 5 to 10 inde …

The paper explaining MCMCglmm indicates the sense in which Hadfield used the term "trait," which isn't quite the same as that recommended by the Wikipedia page. In my experience, I think that in commo …

There really are two questions here. One has to do with correlations among independent variables, the other with correlations among outcomes. To deal with correlations arising from things like pups wi …

If your interest is in long-term trends in eGFR, you should just omit any measurements made during acute illness. Penalize those values completely, as they are unreliable. For those unfamiliar with th …

When you do multiple comparisons you have to correct for the number of comparisons. So if you proceed this way you will have to do a lot of multiple-comparison corrections. One trick is to structure t …

Cochran's Q test is a generalization of the McNemar test when outcomes are binary, as they seem to be in your case (positive/negative infection assessment by either PCR or bacterial culture). Whether …