Hi edgeR authors， I would like to apply the norm.factors calculated in gene expressions by using edgeR pipeline to other expression data, for example small RNA and transposon expression in the same samples. After puting counts and group into DGEList object, I assigned norm.factors to samples$norm.factors and then estimate dispersion. But it seemed that this custom norm.factors didn't work for dispersion estimation, because I got a weird BCV plot with only a few variables (should be 1500 variables) and a lot of "Inf" in the fit$df.prior. I also tried calcNormFactors(x), then replaced the norm.factors by norm.factors from RNA-seq analysis. Still, it did not wok. We have different kind of expression data (gene expression, transposon, small RNA and so on) from the same samples. we would like to use the same norm.factors calculated in RNA-seq DE analysis to other expression data to account for lib.size and composition bias. How can I do this?
Regard. Mingxing Yang