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Could I use the surrogate variable calculated from the whole samples when splitting samples by tissue?
Hi, I am investigating age-related gene expression changes across different tissue regions with RNA-seq data using DESeq2. A part of my coldata looks like(I have a total of 100 samples)
> coldata
tissue age sex
1 PFC 3month female
2 Amy 3month male
3 PFC 6month female
4 Amy 6month male
5 PFC 20month female
6 Amy 20month male
To mitigate technical variation, I've applied SVAseq with n.sv=2 across all 100 samples. For the subsequent differential expression gene analysis, I've constructed the design model as design = SV1 + SV2 + sex + tissue + age. Additionally, I'm considering dividing my data by tissue. However, I'm uncertain whether it's appropriate to use the surrogate variables computed from the entire dataset as adjusted factors for this purpose. Any insights would be greatly appreciated. Thank you.