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 and how? or do I need to convert it to GTF format first?

Look forward to your comments.

Many thanks,
Shirley