Dear Steve,

I have a very large Affy Exon array data including >1000 samples, and I
would like to compare them with RNAseq data.

1. In the SCAN..vignette.pdf, UPC_RNASeq can take read.counts matrix in
which each row is for one gene, and each column for each sample. Is it
possilbe for UPC taking RPKM value as input?

2. My exon array data has been preprocessed using RMA, and adjusted for
many technical variables. So I have a data matrix with gene-level RMA log2
value for each gene across all 1,000 samples. Can I use UPC normalize my
data by directly using this data matrix as an input file.

Many thanks,
Shirley

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