I'm working with RNA microarrays, and I'm a newbie to the field. I processed the results with the limma package for Bioconductor.
I'm trying to decide which fold change threshold I should use. I plotted logFC threshold against the number of differentially expressed genes. I have three conditions, so I got three curves which look very much like reverse sigmoid curves. I've asked colleagues and was told that good quality data usually show such curves but it doesn't imply anything.
So, could use please explain why do they look this way or where could I find any explanation? Then, is it possible to use this data to define log fold change threshold? Do plateau, transition and exponential phase have any biological meaning?
Thanks in advance!