Question: DEseq2 logfold interpretation
0
gravatar for MAPK
11 months ago by
MAPK1.4k
United States
MAPK1.4k wrote:

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

rna-seq deseq2 • 466 views
ADD COMMENTlink modified 11 months ago • written 11 months ago by MAPK1.4k
4
gravatar for h.mon
11 months ago by
h.mon27k
Brazil
h.mon27k wrote:

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.

ADD COMMENTlink written 11 months ago by h.mon27k

Thanks to both of you

ADD REPLYlink written 11 months ago by MAPK1.4k
3
gravatar for afli
11 months ago by
afli190
China, Beijing, IGDB
afli190 wrote:

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.

ADD COMMENTlink written 11 months ago by afli190
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1951 users visited in the last hour