I have a target gene, which is differentially expressed in lung cancer patient, house keeping gene, and a third gene which is highly expressed in all lung cancer patients. I took the fluorescent signal for all the genes after hybridizing them with a particular fluorescent dye. Now I have the raw data for every gene and their concentration. I want to see the concentration difference of the target gene in a patient sample and normal sample. What statistical method should I choose and what data normalization procedure should I follow?
You should compare mean between the patient fluorescence intensity and control (ANOVA)
You have to first normalize the values of third gene by dividing it by the values obtained from house keeping control gene in each sample. Following this, the normalized expression of third gene in cancer patients can be compared with the normalized expression of third gene in normal samples by using a one-way ANOVA followed by a post-hoc analysis such as Bonferroni.
Hello,
there is a number of methods to pre-process your data. You should try all of them to find out the best one for your data set. For example, standard normal variate, multiplicative csatter correction, extended multiplicative scatter correction, generalized least square weigtning filtering.
Best regards
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