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

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