Hi to everyone
(this is my first post here!)
We are interested in detecting which proteins are affected (regulated) when a drug is added to cells.
We decided to perform our proteomic experiment in five different cell lines (with very different genetic backgrounds) to make sure we can find "truly responders" to the drug (and not something that only occurs in one specific cell line). Therefore, we analyzed the proteomes of five cell lines before and after the treatment (all 10 cell samples were analyzed three times, that is technical replicates, making a total of 30 measurements)
One could expect that a given protein might not respond equally in all 5 cell lines, but still, its effect is similar across them (for instance, the protein is increased in all 5 cell lines, but the fold-changes are different: some are larger than others, yet all 5 are positive)
Technically, it is not possible to perform the experiment "before and after" on exactly the same samples (they are obviously different cell culture plates) but considering that each cell line might have a different response to the drug, still similar... would this be a paired experiment? We want to use limma with paired samples and not sure if this is correct for our study.
Thanks a lot
