Certain genes do not get expressed in 'control treatment' or 'control plants', and thus 'Ct' value of such target genes is not obtained in real-time expression experiments (Ct = 0). In such cases, how to calculate fold change expression of target genes in the 'treatment experiments'?
Please consider the following example: I have an empty glass ("control"). Now I fill in some water ("treatment"). Now there is some water in the glass. What is the fold-change of water by the treatment?
A "fold-change measure" is simply not defined when the measured quantity is zero under one of the conditions.
Hence your task is simpler that quantifying a fold-change - it's simply showing the difference in the expression state (yes/no). This may be statistically relaxed to the question if the proportion of samples with detected expression depends on the treatment (binomial or logit model).
Please consider the following example: I have an empty glass ("control"). Now I fill in some water ("treatment"). Now there is some water in the glass. What is the fold-change of water by the treatment?
A "fold-change measure" is simply not defined when the measured quantity is zero under one of the conditions.
Hence your task is simpler that quantifying a fold-change - it's simply showing the difference in the expression state (yes/no). This may be statistically relaxed to the question if the proportion of samples with detected expression depends on the treatment (binomial or logit model).
If it is for the sake of including this gene in clustering etc. you could set the Ct for non-expressed gene to 40. This will give you a high 'fold-change'
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