Deseq2 paird analysis in a cohort mixed of paired and unpaired samples
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@8d7b51c7
Last seen 16 months ago
Germany

Hi fellow DESeq'ers!

I have a dataset of 180 RNA-seq samples for which I run differential expression analysis using deseq2! I have a mixed up of paired samples and unpaired samples: 60 paired samples (30 cases vs 30 controls from 30 patients) and 120 samples unpaired from 120 patients either case and control! I am wondering if I can use the paired analysis offered by deseq2 in this case ? here is my fomrula

formula(~ sequenicng_lane + Patient_id +  status)

Thanks in advance; Fatemeh

DESeq2 RNAseq123 • 654 views
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ATpoint ★ 4.2k
@atpoint-13662
Last seen 13 hours ago
Germany

Please see DESeq2: paired samples + controls

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Thanks. I already saw this but there, the question is somehow different in my case most of the samples are unpaired and they are either case or control!

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