DESeq2 for multiplex qPCR
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ilyaal • 0
@ilyaal-10036
Last seen 8.0 years ago

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

deseq2 • 1.1k views
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Entering edit mode
@mikelove
Last seen 2 hours ago
United States

DESeq2 is exclusively designed for count data. The input values should be counts (0,1,2,...), or rounded estimates of counts. There's no reason to use DESeq2 for continuous data.

I don't have any recommendations for normalization or analysis of multiplex qPCR.

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