Hi Michael,
I've read you paper on DESeq2 (Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2) and have a question about using the same approach for analysis of DNA-barcode quantification data acquired using multiplex qPCR on Fluidigm Biomark. The thing is we have a similar problem as you have with low read counts. So the question is can I use DESeq2 algorithm for multiplex qPCR when the Ct values are converted to read count like values? If not, can I use the same type of normalization using median of ratios approach?
Best
Ilya