Answers.Body: <p>No, you cannot. It is a basic principle of any experiment that you cannot add data from completely unrelated other experiments and expect any meaningful quantitative readout. There is a batch effect between the existing data and the newly-added public data, and since batch and experimental group is the same here you cannot correct for it. Don't do that.</p>
  
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Answers.CreationDate: 2024-04-29T11:16:13.603Z
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Body: <p>I have recently sequenced a bulk dataset. However one of my conditions has a lot of contamination from other cell types. I was thus thinking of using a publicly available single-cell dataset of my cell type of intereset, perform a pseudobulk reduction and integrate the pseudobulk dataset into my bulk RNA seq data.</p>
  <p>Is this possible ? Or would there be way too much transcriptome variation and batch to batch differences ? Can I normalize for batch somehow?</p>
  
Tags: <rna-seq><scrnaseq><rna><transcriptome><batch-effects>
Title: Is it possible to integrate a bulk and a pseudobulk (previously scRNA or snRNA seq) dataset
ThreadText: # Is it possible to integrate a bulk and a pseudobulk (previously scRNA or snRNA seq) dataset
  
  (Asked by: username_0 on 2024-04-29)
  
  I have recently sequenced a bulk dataset. However one of my conditions has a lot of contamination from other cell types. I was thus thinking of using a publicly available single-cell dataset of my cell type of intereset, perform a pseudobulk reduction and integrate the pseudobulk dataset into my bulk RNA seq data.
  
  Is this possible ? Or would there be way too much transcriptome variation and batch to batch differences ? Can I normalize for batch somehow?
  
  **Tags:** rna-seq, scrnaseq, rna, transcriptome, batch-effects
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2024-04-29. Score: 1
  
  No, you cannot. It is a basic principle of any experiment that you cannot add data from completely unrelated other experiments and expect any meaningful quantitative readout. There is a batch effect between the existing data and the newly-added public data, and since batch and experimental group is the same here you cannot correct for it. Don't do that.
  
  
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