Question: DESeq2 confounding cartridge
gravatar for kim.malek88
19 months ago by
kim.malek880 wrote:


I am analyzing NanoString gene expression data with DESeq2. The aim is to identity differently expressed genes between advanced and not advanced renal cancer ("status"). The measurements were carried out in three cartridges, and unfortunately all of the samples with inferior RNA-quality (low RNA-content) were measured in the third cartridge. (Fortunately,  the advanced cancer samples are not significantly over/under-represented in the third cartridge.)

Question: Should the cartridge be included as a confounding variable in the DESeq2 analysis (which model should I use: design= ~ cartridge + status, or design= ~ status)?

ADD COMMENTlink modified 19 months ago by Michael Love25k • written 19 months ago by kim.malek880
Answer: DESeq2 confounding cartridge
gravatar for Michael Love
19 months ago by
Michael Love25k
United States
Michael Love25k wrote:

Yes I would typically add any such batch effect to the design. You can use plotPCA to see the batch effect by cartridge (see vignette).

ADD COMMENTlink written 19 months ago by Michael Love25k
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