Question

differential gene expression analysis

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3.7 years ago

surabhismo ▴ 20

Can I do differential gene expression analysis by using the cases and control data from two different GSEs?

RNA-Seq gene • 1.3k views

ADD COMMENT • link updated 3.7 years ago by Istvan Albert 100k • written 3.7 years ago by surabhismo ▴ 20

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What is GSE ?

ADD REPLY • link 3.7 years ago by GouthamAtla 12k

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May mean different GEO 'GSEnnnnnn' studies

ADD REPLY • link 3.7 years ago by Kevin Blighe 87k

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GEO (gene expression omnibus ) provides different studies each study is identified unique ID i.e.; "GSExxxxx"

ADD REPLY • link 3.7 years ago by surabhismo ▴ 20

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Thanks. Very intuitive.

ADD REPLY • link 3.7 years ago by GouthamAtla 12k

score 3 · Accepted Answer · 2020-08-03

If what you are asking is whether you can compare control and treatment across different experiments then the answer is that you have to more careful (while you are doing it) and more transparent (when disseminating the results) about what you are doing.

The statistical power of most methods will be greatly reduced and you would need to perform more careful error analysis and estimation.

What you are asking about is a variant of meta-analysis, where one combines the results of multiple, prior scientific studies to derive new insights.