Hi, I would to see if there us any gene differentially expressed based on a continous variable (temperature) over age. I want to know exactly if there any genes that differ over age.
I have the following design:
design(dds) = ~ Agegroup:temperature
Agegroup has two factors: 20_40 and 41_70
DESeq(dds)
I obtain the following results:
resultNames(dds) [1] "Intercept"
"AgeGroup_20_40.temperature" "AgeGroup_41_70.temperature"
To get those genes i run:
results(dds,name="AgeGroup_20.40.temperature")
Do i understand correclty this is returning only differentially expressed genes within the group 20_40 ? How do i get those differentially expressed between the two age groups at different temperatures ?
•
written
by
David
1 answer
You need to re-order the levels of your Agegroup variable. In your example, AgeGroup_20.40.temperature is being compared to AgeGroup_41_70.temperature. Perhaps this is already what you want.
Kevin
Log in to answer this question.
-
DESEQ2 Code
written by ananta.kapoor •
-
Strange RNA-Seq Results When Adding Covariates
written by robert.flynn.21 •
-
Time-series RNA-seq analysis using DESeq2
written by Debebe •
-
DESeq factor order
written by Chris •
-
DESeq2 P/Padj values zero?
written by swilson •
-
DESeq2, batch effect correction, multiple conditions
written by Sy80 •
-
check deseq2 design please
written by David •
-
Specific DE comparisons with complex design matrix
written by grant.hovhannisyan
-
Differential gene expression analysis
written by bioinfo456
-
heatmap using DESeq2
written by sumithrasank75
