[BioC] how to set parameter of DESeq function estimateDispersions

wang peter wng.peter at gmail.com
Mon Aug 13 03:58:19 CEST 2012


how to set parameter of DESeq function estimateDispersions
i have 6 groups data and each group contains 3 samples
conditions=c(rep("DL7", 3),rep("DL27", 3),rep("DLCK", 3),rep("L27",
3),rep("L7", 3),rep("LCK", 3))
i will compare them between two groups.

should i use
cds <- estimateDispersions(cds, method =
"per-condition",sharingMode="fit-only") ?
what difference between using per-condition and blind? why say blind
lead to loss of power;

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