Hello,

So, I am working on a data that use fibroblast RNA-seq result. Another samples have multiple experimental duplicates for each data point which is nice. Some have 3 or more and some have 2 duplicates. I believe it is still ok to use 2 duplicates in DESeq2. My problem is that for the original sample, fibroblast, they only provide 1 sample without duplicates. I understand that fibroblast is quite general cell line so I am thinking maybe I can add another fibroblast sample from another dataset so that I can use DESeq2 to analyze the data with comparison to fibroblast. Is it possible to add another dataset?

I maybe need to check for consistency like using clustering in the gene expression level to prove that fibroblast from another data set can be included. Any suggestion for any other method?

Yes, you can add samples from other groups to provide some information for estimation of the biological variability. Then you are basing the results on the assumption that the biological variability per gene is similar across the samples you include in the dataset.