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5.9 years ago
english.server
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Hi there!
Newbie here! I am a biologist and interested in biomarker discovery, starting from raw data, e.g. from gene expression data found at GEO database. Where should I start? Is (in silico) biomarker discovery also called feature selection?
Thank you in advance.
"biomarker from data" is pretty broad. What kind of data do you mean, and what kind of biomarkers are you searching for?
Thank you.I updated my question
What is the ultimate aim of your project? I mean, you want to find some biomarkers, but why? What are the project's 'deliverables'? You may get ideas from my answer, here: A: What is the best way to combine machine learning algorithms for feature selectio
PS - yes, 'feature extraction / selection' can be regarded as biomarker discovery.
Thank you for your response to this thread and your answer on the linked thread. I am interested in finding biomarkers from available data as it is a budget-less way to publish scholarly paperss, which in turn I am in need of!
To still publish from GEO studies, your best option is likely to merge multiple studies together and achieve a large sample n. If you just re-analyse 1 or 2 studies, then you will struggle to publish (except in the 'bogus' journals). An interesting area would be rare diseases, where original studies may have just been a few samples; however, combining these, the sample n can increase.
Also there is power in multi 'omics'. So, look at both expression and methylation data, as an example, and link these up to genotype data that you can additionally find.
Thank you indeed very much for your precious comment. Ill try to follow them.
Have you looked at the tutorials on this site (e.g here). Bioconductor and the widely used limma package for differential expression analysis are also places to look.
Thank you @Ahill for your response. however I am interested in post-DEG analysis.
Maybe add more information in your question, see here how to ask a question that can bring more useful answers.
Thank you @b.nota for your reponse. Ill update my post
Thank you @b.nota for your reponse. Ill update my post