Tool for selecting lncRNA from microarray / RNA seq

Question

[enterid]

I am going to comparing the lncRNA expression data from tumor sample and my own clicial data , the tumor sample i am acessing are microarray profile/RNA seq from these 2 platfrom: IlluminaHiSeq_RNASeqV2 and AgilentG4502A_07_3.

However , i was wondering how i can filter out the known protein coding transcript out and the RNA gene with short length ?