Dear List, I have 50 RNA samples and each sample has the following expression data: 1. Illumina RNAseq 75bp paired-end data 2. Affymetrix Human Exon 1.0 ST array My goal is to compare RNASeq with Exon array data at the gene-level and exon-level. To be fair, I was suggested to generate RPKM/FPKM value for each gene and exon using the Affymetrix Exon/Probeset annotation file. From Affymetrix website, I selected "Human Exon 1.0ST array", then downloaded the probeset/exon-level annotation file named "HuEx-1_0-st-v2.na32.hg19.probeset.csv". I have two questions: 1. Is this the right file to use? 2. If it is, should I directly use it to generate FPKM for my RNAseq data quantification using Cufflinks or other tools, or do I need to convert it to GTF format first? Look forward to your comments. Many thanks, Shirley [[alternative HTML version deleted]]