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uc-bd2k / GREIN

GREIN : GEO RNA-seq Experiments Interactive Navigator
https://shiny.ilincs.org/grein
GNU General Public License v2.0
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Gene number different from different dataset #13

Closed ngutrinh closed 3 years ago

ngutrinh commented 3 years ago

I got the results from some different dataset. however, the gene numbers in the count table were different. For example GSE55807: 28,089 genes, and GSE126669: 28,125 genes. Can I combine results from multiple datasets for further analysis? Thank you.

Mario-Medvedovic commented 3 years ago

Yes, you can combine the results. The differences come from two versions of mappings between the Ensembl transcript ids and Entrez gene ids. Underlying processing pipeline for transcript quantification is identical for all datasets, and data for the overlapping genes would be the same regardless of which annotation is used. Mario

ngutrinh commented 3 years ago

Yes, you can combine the results. The differences come from two versions of mappings between the Ensembl transcript ids and Entrez gene ids. Underlying processing pipeline for transcript quantification is identical for all datasets, and data for the overlapping genes would be the same regardless of which annotation is used. Mario

Yes, Thank you so much for your response Mario-Medvedovic, I have one more question about combination results, as I know a combination of the different dataset will get the batch effect. I want to ask how to avoid the batch effect when combining result from GREIN? actually, I want to combine gene count or normalized count results. Thank you