DESeq2 confounding cartridge
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@kimmalek88-15334
Last seen 3.3 years ago

Hi,

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)?

deseq2 confounders nanostring rnaseq differential gene expression • 540 views
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@mikelove
Last seen 5 hours ago
United States

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).

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