Microarray data analysis

Question

[maki.dur]

Hi friends,

Currently, I am working on some microarray data analysis (ICGC database) and I need to calculate log ratio between gene expression of tumor tissue and normal tissue. I have somthing like this:

patient1 - normal tissue: gen1: -0.78, gen2: 0.487, gen3: 1.147 and so on

patient1 - tumor tissue: gen1: 1.87, gen2: 1.47, gen3: -0.147 and so on

patient2....

Equation of log ratio is: LR = log2(P/Q), in my case P - tumor tissue, Q - normal tissue

LR(gen1) = log2(-0.78/1.87)

Any idea how to dealing with negative value in log? Or I am doing this on a wrong way?

Answer 1

[vivekbhr]

If you are looking at raw intensity measures, they will have some negative values. However negative intensity doesn't mean anything and should be interpreted as zero. so you can replace them with some small +ve value or 1 (so that it's easy to divide or take log).

Hope this was useful.