Question: DESeq2: DESeq2 interaction term study result interpretation
gravatar for Gyan Prakash Mishra
7 months ago by
Gyan Prakash Mishra0 wrote:


I have RNAseq data from two conditions in two different genotypes. I have put the same design as explained in mannual of ?results.

I am interested to know the effect of condition between two different genotype.

Below is the code that i followed

> condition <- factor(c(rep("Uns",4),rep("treat",4)),levels = c("Uns","treat"))
> genotype <- factor(c(rep("WT",2),rep("KO",2),rep("WT",2),rep("KO",2)),levels = c("WT","KO"))
> coldata <- data.frame(condition,genotype)
> coldata
 condition genotype

1       Uns       WT
2       Uns       WT
3       Uns       KO
4       Uns       KO
5     treat       WT
6     treat       WT
7     treat       KO
8     treat       KO

> design <- ~ genotype + condition + genotype:condition
> dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=design)
> dds <- DESeq(dds)
> res <- results(dds, name="genotypeKO.conditiontreat")
> resdata <- merge(,, normalized=TRUE)), by="row.names", sort=FALSE)


gene_symbol baseMean log2FoldChange lfcSE stat pvalue padj WT_Uns_R1 WT_Uns_R2 KD_Uns_R1 KD_Uns_R2 WT_treat_R1 WT_treat_R2 KD_treat_R1 KD_treat_R2
Ifitm3 25243.3710308171 -1.8595537198 0.4059027452 -4.5812789935 4.62140822664497E-006 0.0003178812 1232.0353939289 2575.4130590755 9985.2629327363 11908.9251219533 33107.2809424779 35049.6340180347 49770.5146124143 58317.9021659157
Il12b 41756.9595852118 -2.7316128291 0.5936250651 -4.6015793296 0.000004193 0.0002909209 3.7696136479 3.9682789816 15.5654917112 15.5875983272 83419.6492515375 124140.55396696 60403.6485961083


If I look at these two gene, based on "log2FoldChange" value, both seems to be downregulated, but if look at count normalized value in WT and KO, the value is quite opposite. Why is this so, am I missing something here.  could someone please explain this analysis.

Thanks in advance !

deseq2 • 208 views
ADD COMMENTlink modified 7 months ago by Michael Love23k • written 7 months ago by Gyan Prakash Mishra0
Answer: DESeq2: DESeq2 interaction term study result interpretation
gravatar for Michael Love
7 months ago by
Michael Love23k
United States
Michael Love23k wrote:

You are using an interaction term in the design, and testing the interaction term. This is not a main effect. Please see the diagram in the vignette section on interactions.

ADD COMMENTlink written 7 months ago by Michael Love23k

Thanks Michael ! 

Sorry I didn't read it carefully ! Now I understood why its so. It was really helpful !  

ADD REPLYlink written 7 months ago by Gyan Prakash Mishra0
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