Dear Bioconductor support team,
I have samples from two time points namely V1 and V4. The samples belong to two categories: Treatment and Placebo as follows:
005v1 Placebo 005v4 Placebo
008v1 Treatment 008v4 Treatment
The ID number 005 etc represent the same sample at two time points. At V1 time-point there is no treatment given, its just that the samples are assigned to be given a treatment (treatment) or not (placebo). At V4 time-point there would be difference in placebo and treatment sample.
Now, if the question is to identify the changes caused due to the treatment, how should I define the design? Should V1 time-point be taken into consideration or not, given that the treatment intervention was given only after the assignment of samples at V1.
It seems like a paired analysis, where the blocking factor is the IDs of the samples, but I'm not sure of setting up the design. Could someone give suggestions. Thanks in advance!