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Hello,
I am doing single cell RNA-seq analysis. I have 2 groups of samples: Test and WT. For both groups, I have 2 different data: treated and untreated. My samples are a composition of various cell types, but each of my samples have the same variety of cell types (The samples are taken from the same tissue, so each sample has same composition. But they consist of various cell types, it is not cell-line.)
I want to compare:
untreated WT vs treated WT
untreated WT vs untreated Test
untreated Test vs treated Test
treated WT vs treated Test
My question is, is it a good idea to do the analysis of the data in the same seuratobject? For example, by using multifactor integration into a single seuratobject? Or should I make separate seuratobjects for the variables?
I am worried that the clustering and DEGs will get affected if I include everything into a single seuratobject. (I want the clustering to be by cell types) But the DEGs will probably be different before/after treatment.
Thank you
I am doing single cell RNA-seq analysis. I have 2 groups of samples: Test and WT. For both groups, I have 2 different data: treated and untreated. My samples are a composition of various cell types, but each of my samples have the same variety of cell types (The samples are taken from the same tissue, so each sample has same composition. But they consist of various cell types, it is not cell-line.)
I want to compare:
untreated WT vs treated WT
untreated WT vs untreated Test
untreated Test vs treated Test
treated WT vs treated Test
My question is, is it a good idea to do the analysis of the data in the same seuratobject? For example, by using multifactor integration into a single seuratobject? Or should I make separate seuratobjects for the variables?
I am worried that the clustering and DEGs will get affected if I include everything into a single seuratobject. (I want the clustering to be by cell types) But the DEGs will probably be different before/after treatment.
Thank you