I've been battling for months to work out which statistical test is the best way to make the most out of the data I have. I have been measuring depth related changes in a material. At depths of 2mm (0-2mm, 2mm-4mm etc) for 10 slices I have measured several quantitative parameters. I want to compare differences in these parameters at different depths and also between the different ages and sexes.

I tried PCA but that was inconclusive, we tried multiple linear regression but decided this wasn't appropriate as the measurements can't be deemed independent, we also tried two-way ANOVAs but we're unsure if this is appropriate. As you can imagine, we have a lot of data and want to make the most of it. I have been using Rstudio for my analysis.

I hope this makes sense, I'm happy to add any information that is needed! Thanks in advance