What does mean?
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Entering edit mode
11 months ago
Angel ★ 4.1k

Hello

In time series I am confused about some definitions

In DESeq2 tutorial

library("fission")
data("fission")
ddsTC <- DESeqDataSet(fission, ~ strain + minute + strain:minute)


Can somebody please tell what this mean

The following chunk of code performs a likelihood ratio test, where we remove the strain-specific differences over time. Genes with small p values from this test are those which at one or more time points after time 0 showed a strain-specific effect. Note therefore that this will not give small p values to genes that moved up or down over time in the same way in both strains.

ddsTC <- DESeq(ddsTC, test="LRT", reduced = ~ strain + minute)
resTC <- results(ddsTC)


Am I right that means only we will have genes related to the difference of strains and we removed genes related to changing over time??

DSEeq2 R • 306 views