Off topic: Tool/how can i selecting lncRNA from microarray / RNA seq profile

Question

[enterid]

i am going to comparing the lncRNA expression data from the tumor sample and my own clinical data , the tumor sample i am accessing are microarray profile/RNA seq from these 2 plant from: 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 ?