Microarray Study Design - (Mar/18/2012 )

HI,

I am writing to seek advice regarding microarray study design.

I have 5 cancer cell lines: 1 cell line is normal and 4 are cancer related. My question relates to whether a normal versus cancer analysis using these arrays would have sufficient power to detect a difference between normal and cancer cell lines. Would this study be worth doing? I have previously read that you need at least 5 samples per group to find differences between groups. Is this correct?

Please advise what is the best course of action in this instance.

Thank yo in advance for your help.

hi Casey,

how similar are those cancer cell liines? would you expect to find any differences among them compared to normal cells? i don't work with cancer stuff, but i assume that the mechanisms might be similar among those cells...

about the question that you need at least 5 samples, do you mean biological replicates? it's like any other analysis, the more replicates you have, the more reliable your data will be. after working with microarray data I found many significant differences between treatments by using only 3 replicates, however, each replicate consisted of the RNA exctracted from 2 independent individuals from the same treatment.

currently microarray chips are lot cheaper than they used to be. is your study novel? I could almost place a bet that there are already cancer-related microarrays publicly available. so investing in an experiment of this kind is only as worth as the novelty that it represents.

hope this is useful. good luck!

tj.