I have 6 RNA-seq samples like this
4 patients (005, 036, 121, 013) I have 3 tumour samples and 3 cancer models (organoid)
This is PCA of log transformed data by DESeq2 (tumour Vs. organoid)
In this paper https://www.nature.com/articles/s41467-018-05190-9
They are saying
Finally, for each patient, the genes that are specifically up- or down regulated in each patient’s organoid (1 vs. all comparison, p ≤ 0.05 and abs (log2-FoldChange) ≤ 1) and that are among the top-50 genes with highest base mean expression were selected.
They have tumour and organoid like my case; My confusion is what they mean by "each patient’s organoid (1 vs. all comparison"? Because like them I need up or down regulated genes in each patient's organoid but I can not figure out I should compare each organoid versus what?
The ultimate goal would finding a signature of genes specific to each organoid as each organoid originates from tumour of a patient by these signatures one would be able to classify cancer to sub types