In a RNA-seq dataset, I have two batches that have one sample in common, plus other samples in each batch. There are 3 replicates for each sample. Is there a way to compare other samples across tthe two batches? In other words, how can the batch effects be removed?
The short answer is yes, you can use even a single sample to estimate the batch effect (and therefore control for it in otherwise confounded comparison).
However you have low power with a single sample, as compared to an orthogonal (balanced) design. This is because there is substantial variance from using the single sample to define the batch effect, and therefore also the condition effect.
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version 2.3.6
Yes, you can perform DEG analysis across two batches with one shared sample by using batch correction methods like ComBat or limma. These tools help normalize batch effects while preserving biological differences. 7 brew locations