I have a tabular dataset containing counts, which looks like this:
ID Gene Ctrl_1 Ctrl_2 Ctrl_3 TMZ_1 TMZ_2 ... Hyp_3 1 AAA 200 300 212 231 123 ... 231 2 BBB 100 231 3 123 99 ... 88 ... 5000 ZZZ 30 999 54 3 2 ... 12
Each row represents a particular gene that is silenced. The numbers in the remaining columns represent how many cells are still alive after waiting 10 days in each of the three conditions "Control", "Temozolomide" and "Hypoxia", when a given gene was silenced. For example: when gene AAA was silenced, ten days later there were 231 cells that were still alive in the one sample treated with temozolomide (TMZ_1).
The aim is to find the genes that can be silenced such that there is a significant reduction in the number of living cells, from control to treatment.
My question is, what statistical test should one use to compare these results? I think that Table 1 in this article (http://www.ncbi.nlm.nih.gov/pubmed/19644458) might be helpful, but I don't know which to pick. Can anyone help?
(Edited for clarity)