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Question: DESeq2 for multiplex qPCR
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gravatar for ilyaal
18 months ago by
ilyaal0
ilyaal0 wrote:

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

ADD COMMENTlink modified 18 months ago by Michael Love14k • written 18 months ago by ilyaal0
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gravatar for Michael Love
18 months ago by
Michael Love14k
United States
Michael Love14k wrote:

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.

ADD COMMENTlink written 18 months ago by Michael Love14k
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