Hi there,
I have qPCR results from 6 target genes and a housekeeping gene. Each different gene had its expression measured after 3 different treatment conditions and a non treatment control.
I have log 2 transformed the fold changes that were the result of normalising the different treatments to the housekeeping gene and non treatment control.
My question is, how does one present this on a graph. Is it necessary to leave a space for the non treatment control, given that all its values will equal to zero (log2(1) = 0)?
Also, does a one way ANOVA work for statistical analysis? But am I correct in saying that performing an ANOVA will only show statistical difference between different treatments, but not whether the treatment decreases or increases the expression?
Yes, the ANOVA only tells you that there is an effect. It does not tell you the magnitude of the effects or their direction. ANOVA is typically paired with other methods to better understand relationships.
You corrected the data relative to the control. The control then gets dropped from the analysis. Include this step in the methods and remind readers in figure/table legends that the results are corrected not raw. Do not confuse the two in results and discussion. "There was a 17% decrease in expression in treatment B relative to A in the control adjusted data" may not be the same as "there was a 17% decrease in treatment B relative to A."
Presenting the results on a graph depends on what you want to show and what sort of data you have. What are the replicates? Are you trying to optimize the qPCR reaction and comparing reaction kinetics, or are you comparing CT values?
Timothy A Ebert
Thank you for your answer Timothy. I want to compare the treatment both to the control and to each other. The thing is, some of my treatments are not statistically significant when compared to the untreated control. I originally thought it would be visually better to have just a column in the graph with the dots placed at zero for the untreated control. But from your answer I gather it is standard practice to just drop the control column and mention in the figure legend that it was not statistically significant.
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