I am doing one analysis where I have 9 different conditions and only two options as outcome. I have done a pearson chi-square test, and in some of the cases I violated the assumption that expected counts should be greater then 5. What should I do? In the same test I had asked for the Fisher exact test p-value, can I use this p-value to all the cases or should I run another analysis only with those that violated the assumption of the expected counts?
I would simply use the Fisher exact p-value for in call cases. You already have the values. This is a well accepted test that will be reliable in all cases. Unless the counts are small, Fisher's exact test and Pearson chi-square will give similar results anyway.
I work in the biomedical genomic research and one hardly never sees a Pearson chi-square test in that literature. Fisher's exact test is standard.