[BioC] edgeR calcNormFactors for paired counts

[Christopher T Gregg]

Hi,

We are examining the use of edgeR to analyze allele-specific count data from RNASeq experiments.  In these studies, each biological replicate (n=18) has two columns: one with counts from the maternal allele and the other with counts from the paternal allele for each gene.  Thus, the data is paired since these counts are parsed from the data for each each replicate.  We wish to fit a glm to the data that tests for a main effect of the allele (counts ~ replicate + allele)  to find genes that exhibit a significant allele expression bias.

My question relates to how to best handle the normalization of the counts in this case.  EdgeR applies calcNormFactors to the columns, which disrupts the maternal:paternal count ratio for each gene in each sample.  We are grateful for advice on how to best manage the analysis of this type of data.

best wishes,
Chris