Hi there,
I have an experimental design with 2 factors (concentration and time) with repeated measures (i.e. the same subject is tested for each combination of factors).
I have tried the 2way ANOVA analysis after uploading my data as time series + one factor and I click to include the interaction term that says it is repeated measures but I don’t see anywhere to input what column to repeat by. Is it automatically blocking (or doing the repeated measures) on the Subject column in the metadata? Or is the term “repeated measures” used differently here?
Also, when I upload my data like this, many proteins are significant to concentration (main factor) and the interaction, but time comes up as 0. Is this something that happens due to the nature of the time series data format? Or perhaps it is true that none change with time in my analysis. When I upload the data as multivariate and put time as a different categorical factor, only 3 come up as significant under time while the other factor and interaction are 0. So now I am wondering what the difference is in analysis when I upload the same data but in different formats.
I’ve also tried the limma analysis but I don’t think that Time counts as a covariate and so there doesn’t seem to be a way to include the two factors.
Thank you for the help and advice!
Sarah