I received a set of microarray data that has already been processed and normalized by the microarray core facility (essentially a matrix with probe IDs, expression values for each sample and a note if the gene is 'expressed over background').
The experimental setup is as follows: we have 3 groups, 6 subjects per group, and each subject was sampled 3 times (T1, T2 and T3) over a course of a month (with intermediate interventions) - so the data is paired. The comparison I want to make is T2vT1, T3vT1 and T3vT2 within each group (to see how the gene expression changes upon intervention), and I want to calculate Log2FC and p-values to produce volcano plots.
I assume the best R package for this type of analysis is limma - however I cannot find a way how to import normalized data into it, and where to start the analysis.
Any help or thoughts would be greatly appreciated!
Thanks in advance.