Entering edit mode
2.5 years ago
JB lee
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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.
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?
TCGA data is RSEM normalized count data downloaded from GDAC and GEO data is expression profiling by array data.
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.
I also agreed there is no benefit of combining different sets. I decided not to try it. Thank you for your help and comment:)