Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
0
0
Entering edit mode
3.7 years ago

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 r newbie • 983 views
ADD COMMENT
1
Entering edit mode

"biomarker from data" is pretty broad. What kind of data do you mean, and what kind of biomarkers are you searching for?

ADD REPLY
0
Entering edit mode

Thank you.I updated my question

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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!

ADD REPLY
2
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thank you indeed very much for your precious comment. Ill try to follow them.

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Thank you @Ahill for your response. however I am interested in post-DEG analysis.

ADD REPLY
1
Entering edit mode

Maybe add more information in your question, see here how to ask a question that can bring more useful answers.

ADD REPLY
0
Entering edit mode

Thank you @b.nota for your reponse. Ill update my post

ADD REPLY
0
Entering edit mode

Thank you @b.nota for your reponse. Ill update my post

ADD REPLY

Login before adding your answer.

Traffic: 1225 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6