Combine GEO ids

Question

[anasjamshed]

I have the following geo IDs:

• GSE230470 ---> Calorie Restriction Outperforms Bariatric Surgery in Reversing Obesity-Driven Tumor Progression in a Mouse Model of Triple Negative Breast Cancer-Study1_tumor
• GSE230471 ---> Calorie Restriction Outperforms Bariatric Surgery in Reversing Obesity-Driven Tumor Progression in a Mouse Model of Triple Negative Breast Cancer-Study2_tumor
• GSE174761 ---> Bariatric surgery reduces obesity-associated breast cancer and enhances response to immunotherapy [Tumor - breast cancer RNA-seq]
• GSE202330 ---> Various forms of calorie restriction, but not a nonrestricted low-fat diet, reverse obesity-associated tumour growth and lung metastasis in a mouse model of triple-negative breast cancer-RNAseq
• GSE28713 ---> Obesity Promotes Epithelial-To-Mesenchymal Transition and Tumor Progression in a Mouse Model of Claudin-Low Breast Cancer
• GSE151866 ---> Tumor genes regulated in obesity-mediated breast cancer

Can we combine all of these ids together to find differentially expressed genes?

[Ram]

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Answer 1

[ATpoint]

You have many studies and want to find DEGs. Generally, one does not combine studies into a single differential analysis but analysis per study and then runs meta-analysis to make a statement which DEGs are reproducible across studies. Google meta-analysis for RNA-seq. There are packages out there for this, for example MetaVolcanoR or RobustRankAggreg, and probably many others as well.