| The CT (cycle threshold) value of a given gene represents the PCR amplification cycle at which the gene is detected above a certain threshold. Thus, higher CT values correspond to lower gene expression levels. The typical way to treat CT values is to subtract the CT value of a housekeeping gene, to get dCT values. Again, a higher dCT value corresponds to lower expression, and many values will be negative (for genes that are more highly expressed than the housekeeping gene). This is normal. The dCT values should not be log-transformed, since they are already on the "log-scale" in the sense the abundance of the gene is proportional to 2^(-dCT). So they can be used directly for PCA and linear models to look for differences between groups or association with a continuous phenotype. |
