Is it feasible to combine TCGA and GEO data by using ComBat?
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6 months ago
JB lee • 0

Hi, I want to combine these two data sets from different experiments.

When I search for this, many experts didn't recommend to use Combat.

What is the best way you recommend to merge these two sets?

Or, if you consider it as a terrible idea, what's the reason?

Thank you.

ComBat • 495 views
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There can be no answer to your question considering how you have not explained the data-types that you intend to merge /combine. Which GEO data? - bulk RNA-seq?; cDNA microarray?; scRNA-seq? Which TCGA data? - HT-Seq raw counts?; FPKM expression levels?

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TCGA data is RSEM normalized count data downloaded from GDAC and GEO data is expression profiling by array data.

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Can I ask what is the benefit of combining the studies rather than looking at them individually? I would urge caution over combining unrelated (institution/author/study) data sets as you would be introducing alot of variables.

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I also agreed there is no benefit of combining different sets. I decided not to try it. Thank you for your help and comment:)

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