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Hi,

I have 8 samples with gene expression data, coming from 4 subjects, before and after treatment. I would like to get the overall differential expression before and after treatment, and also the differential expression per subject. I understand that I cannot do statistics "per subject". Is there any way to display the contribution per subject to the overall differential expression?

many thanks, Martijn Huynen

If you have paired data you should block on subject, which is algebraically the same as fitting a model on the difference between treated and control, within subject. You could then generate a heatmap of the logFC for the significant genes if you like.