[DESeq2] setting LFC threshold
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Shail • 0
@dba6855a
Last seen 25 days ago
Hong Kong

Hi,

I want to set the p-value and LFC threshold to DESeq2 output results

The way i understood is

independentFiltering = TRUE,alpha = 0.001 #will filter results for p-value 0.001.


However, how to set an LFC threshold of 1.5. Is it lfcThreshold = 1.5?

Also, how to identify upregulated and downregulated genes.

The summary list by the p-value of DESeq2 run is as follows

res <- res[order(res\$padj),]


In this, I assume the genes with negative LFC are downregulated. But in which group LD1 or control?

DESeq2 • 131 views
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@mikelove
Last seen 1 hour ago
United States

However, how to set an LFC threshold of 1.5. Is it lfcThreshold = 1.5?

This depends entirely on what is a relevant effect size for your experiment. 2^1.5 is a pretty large change. I sometimes recommend log2(1.5) ~= .585 to start, as this covers when expression goes up or down by 1.5.

which group LD1 or control?

See the vignette or workflow for details like this. Note that the answer is printed above the table: LD1 vs control.

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Thank you for the help