I am working on cancer related gene expression data from RNA-seq(RPKM). What I want to do is finding some important gene from gene expression data set, such as genes highly related to tumor recurrence.
But I found that still most of paper working on this kind of research used data set from Microarray, instead of RNA-seq. It has been long time since RNA-seq introduced, and as I know, RNA-seq data is generally less noisy than that of Microarray. Also, now it seems to be enough(although much less than Microarray) RNA-seq data is available, at least for tumor analysis.
Is there any other reason for using Microarray instead of RNA-seq? Are there some critical cons in using RNA-seq gene expression data?