Question: DESeq2 model with blocking factor + interaction term
0
4.2 years ago by
da.de10
Austria
da.de10 wrote:

Hi,

I am using DESeq2 for the analysis of my RNAseq data. I have the following sample set up:

Condition         Treatment
Luc2                   no
Luc2                   DOX
ProtA                 no
ProtA                 DOX
ProtB                 no
ProtB                 DOX

A cell line inducibly expressing one of the 3 different proteins after DOX treatment. Luc2 = negative contol. ProteinA and ProteinB = proteins of interest.

I am using the following model including an interaction term to correct for differences in the cells without DOX and the following results functions to extract the specific DEG for ProtA and ProtB:
design=~Condition +  Treatment + Condition:Treatment

dds <- DESeq(dds, betaPrior=FALSE, minReplicatesForReplace=Inf)

res1 <- results(dds,name="ConditionProtA.TreatmentDOX", cooksCutoff=FALSE, independentFiltering=FALSE )

res2 <- results(dds,name="ConditionProtB.TreatmentDOX", cooksCutoff=FALSE, independentFiltering=FALSE )

I do have three replicates. The libraries from replicate1 were done on day1 and the libraries form replicates2+3 on day2.

If I do a PCA plot using rlog transformed counts I clearly see a batch effect --> best separation according to library prep Day1 and Day2.

Therefore I want to include a blocking factor in the design model.

Is it correct if I just change the design as follows?

~LibraryDay + Condition + Treatment + Condition:Treatment

Best, Dagmar

deseq2 model • 1.5k views
modified 4.2 years ago by Simon Anders3.6k • written 4.2 years ago by da.de10
Answer: DESeq2 model with blocking factor + interaction term
0
4.2 years ago by
Simon Anders3.6k
Zentrum für Molekularbiologie, Universität Heidelberg
Simon Anders3.6k wrote:

"Is it correct if I just change the design as follows?

~LibraryDay + Condition + Treatment + Condition:Treatment"

Yes, this should do what you want.