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Hi all,
I have single-cell data with 3 samples from tumor A and 3 samples from tumor B. For each tumor, I'm only interested in the malignant cell types, which were already identified. I simply want to compare the expression of those malignant cell types between tumor A and tumor B. My initial thought would be to do a differential expression analysis of malignant cells between tumor A and B (using the recommendations for single-cell analysis from DESeq2, for example, or edgeR). As I'm not familiar with single-cell analysis, I'm wondering if this makes sense.
I would appreciate it if someone could give some tips about how to make this analysis.
Yes, I took this chapter as reference. But I'm struggling with the
aggregateAcrossCellsfunction, as I have only one cell type. So I'm wondering if this is necessary or I could use deseq2 or edgeR for this kind of contrast.You could supply a dummy variable to
idsthat has the same value for all cells you want to compare.Nice, it worked. Thank you! :)