DEseq2 logfold interpretation
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2
Entering edit mode
3.0 years ago
MAPK ★ 1.9k

Hi All, I need some help interpreting my DEseq2 results. Here is a bit of my DEseq2 code:

dds$cond <- relevel(dds$cond, ref = "C")
dds = DESeq(dds, fitType = "parametric")
my.names<-resultsNames(dds)
my.names
[1] "Intercept"   "cond_T_vs_C"

Then I did:

res<- results(dds, contrast=list( "cond_T_vs_C"), test="Wald")

Now looking at the result, for this particular gene I have:

baseMean log2FoldChange     lfcSE      stat      pvalue        padj
Seq_483975_2034 1995.245      -1.354257 0.4045764 -3.347346 0.000815893 0.005723768

Can someone please explain me whether this gene is down regulated in Control (C) or in Treatment (T)? Thanks

DEseq2 RNA-Seq • 1.2k views
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4
Entering edit mode
3.0 years ago
h.mon 33k

Use the plotCounts() function to inspect the gene of interest, you'll be able to see then if the gene is up- or down-regulated.

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0
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Thanks to both of you

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3
Entering edit mode
3.0 years ago
afli ▴ 190

This means treatment is lesser than control by a log fold change of 1.354. You can check this by

counts(dds, normalized=TRUE)

you can see the normalized counts of control and treatment.

Aifu.

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