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Statistical analysis of quantitative real-time PCR (qRTPCR) - Statistics on qRTPCR data (Jan/08/2007 )


I have run statistical analysis on fold-changes in a particular gene expression ( n=3 in duplicates). I have two factors in my analysis ( such as STRAIN OF ANIMAL and DAYS OF EXPOSURE TO TREATMENT). Hence I performed two-way repeated ANOVA. Although the fold-changes in gene expression are highly elevated in a particular group ( ex: 100 fold in one group compared to 2-3 in another), I do no thave any statistical significance. I am really puzzled as to how best to represent this biologically relevant yet statistically insignificant data.

Thank you


Hi CC,

why did you choose a repeated ANOVA? Did you take samples from the same animal at different time points? If not, use a 2-way ANOVA for independent samples.
Generally, a two-way ANOVA does three comparisons (Factor 1, Factor 2 and Factor 1 X Factor 2 interaction) which leads to a lot of degrees of freedom and therefore you need a large sample size. Like you experience, even large differences can have very small statistical effect. What to do now? (a) enlarge the sample size, or (cool.gif ask the right question (which factor is important?) and test only for this... but a is defenitely preferable! And another short remark - if you use a measure like time as factor, than you'll have a lot of comparisons! Try to build a general linear model with animal strain as fixed factor and time as covariate, this will suit your data better...

Hope that helps,



Hi Krümel,

Thank you very much for your valuable suggestions