I work both on RNAseq data ( 10 tissues) and Microarray data ( 70 tissues) . The problem is that I find microarray data to be false negative for many of the housekeeping genes. The ratio of tissue-specific to housekeeping genes from RNAseq data comes around 1:10 whereas by microarray it comes 1:2 . This is a huge difference and I don't know which one is more reliable.What is the ratio of tissue-specific to housekeeping genes in the cell? Which dataset I should consider for my study?
If it is human you could compare your results with the ENCODE data or in general with data from ArrayExpress and run the same calculations. Assuming you have chosen a reasonable cutoff for your detection level (signal detectable with high probability above noise level, but arbitrary cut-offs are problematic, and MAs are not good to measure absolute expression), it doesn't look surprising to me that RNA-seq should have 5x higher dynamic range; house-keeping doesn't really mean they are all highly expressed, does it? There are also pitfalls with the array designs (e.g. using suboptimal reporter sequences on the array, which platform is that anyway? Affymetrix?)
Also, I would run a (rank) correlation analysis of the expression values for different groupings of genes: all, somewhat arbitrary 'housekeeping', highly/ lowly expressed genes.
Maybe, if you give provide more details about your experiment, others can say more.