Handling RNA-seq samples from the same individual in DEseq2 analysis
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Entering edit mode
9 weeks ago
gspirito ▴ 10

Hello everyone, here's my question:

I have a dataset of RNA-seq data, where I have gene counts of different tissues from the same individuals in two conditions, like so:

enter image description here

In order to perform a differential expression analysis with DEseq2, comparing KO vs. WT of both tissues together, would it be correct to use this design?:

ddsFullCountTable <- DESeqDataSetFromMatrix(countData = counts.txt, colData = metadata.txt, design = ~Individual+Group, tidy=TRUE)

Thank you in advance

DEseq2 RNA-seq • 152 views
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Entering edit mode
9 weeks ago

Yes, that'd be the appropriate design if you want to account for differences between the individuals.

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