I have two sets of complex qPCR data,

Data set 1 (cell line) with factors: Experiment (1-3), cell replicate (1-3), treatment (versus control), RT replicate (1-3) and qPCR replicate (1-2), measuring 16 different genes in each sample. Efficiency corrected relative quantities have been normalised for the three most stable reference genes.

Data set 2 (clinical) with factors: Patient (1-6), anatomical position (1-4), RT replicate (1-3) and qPCR replicate (1-2), measuring 13 different genes. Efficiency corrected relative quantities have been normalised for the three most stable reference genes.

What is the best way to assign variability attributed to each different factor? (I don’t have access to any paid-for stats packages and extremely limited capability/experience with R).

Any suggestions?

Thanks in advance!