Creating DESeq object and choosing a contrast
1
0
Entering edit mode
Dev Raj • 0
@70c54c57
Last seen 21 months ago
Nepal

I am new to this RNAseq world

I want to perform differential gene expression analysis using DESeq2. I read the DESeq2 vignette but got confused in the Contrasts and Interaction section.

My metadata consists of 22 samples of adipose tissue, 12 from high diet-fed mice (HFD) and 10 from chow-fed mice (CD) each co-cultured with tumor (T) and control (C).

This is the meta data

I have seen that adipose tissue from HFD already differs significantly from adipose tissue from CD (without tumor) but I want to test and filter out only those differences that resulted due to tumor co-culture in HFD compared to CD.

I used the following code to create the DESeq object

dds <- DESeqDataSetFromMatrix(countData = main_data, colData = meta_data, design = ~treatment + tumor_status + treatment:tumor_status) 
dds <- DESeq(dds)
resultsNames(dds)

[1] "Intercept"                  "treatment_HFD_vs_CD"        "tumor_status_T_vs_C"        "treatmentHFD.tumor_statusT"

Is my approach of creating the DESeq object correct ? Also which contrast will give me the desired result?

DESeq2 • 485 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 11 hours ago
United States

If you've read over the section on interactions and are still confused what these terms mean, I'd recommend consulting with a statistician or someone familiar with linear models in R. Picking and interpreting the results table is a key part of the experiment.

ADD COMMENT

Login before adding your answer.

Traffic: 809 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6