Currently I'm trying to compare differential expressed gene from microarray and RNA-seq. I have two categories, A and B for each microarray data and RNA-seq data. My hypothesis is, the DEG list for each micorarray and rna-seq will pretty much same, maybe several difference but not too many. For example, if a set of genes is down regulated from microarray, I will expect same result from RNA-seq. Currently, the result is less than half has similar DEG. Around less than 8000 from more than 16000 genes I checked. I don't see how much it is changed, but I just want to check the same up regulated or same down regulated or same level. As for the data, I downloaded the data from NCBI GEO and it is from different experiment (independent experiment) but both said it is from same cell type. With that difference in experiment, of course there will be difference. My question is, what is your opinion in this case in term of biological meaning? I want to use this as a basis of my comparison to other data set. If the basis is not reliable, I don't know if my result will be valid.
Edit: information about cut off
I forget to add information how I filter the up, down, or similar expression level. So, basically, my cutoff is an arbitrary one. I define like this:
Up regulation : logFC less than -0.75
Similar regulation : logFC between -0.75 to 0.75
Down regulation : logFC more than 0.75
I used Limma for both microarray and RNA-seq data to get the logFC.