Hi
I am analysing differentially expressed miRNA in human plasma (4 groups). I have used the miARma-Seq pipeline (http://miarmaseq.idoproteins.com/) and DESEQ2 for the differential expression analysis.
We used a spike in control (c. elegans miR 39).
Can anyone advise the best method for standardising/ normalising the data to the spiked c.elegans miRNA.
Not sure if I should be using a different pipeline or if there was an established/validated means of doing this?
PC
1 answer
The DESeq2 normalization function estimateSizeFactors has an option to provide "control genes" which you can use here,
type ?DESeq2::estimateSizeFactors to see the help:
controlGenes:
optional, numeric or logical index vector specifying those genes to use for size factor estimation (e.g. housekeeping or spike-in genes)
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