Question: Good tutorials/textbooks/articles to introduce biomarker discovery to a biologist?
0
gravatar for english.server
12 weeks ago by
Germany
english.server140 wrote:

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.

newbie biomarker R • 310 views
ADD COMMENTlink modified 21 days ago by Biostar ♦♦ 20 • written 12 weeks ago by english.server140
1

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

ADD REPLYlink written 12 weeks ago by Benn6.6k

Thank you.I updated my question

ADD REPLYlink written 12 weeks ago by english.server140
1

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 REPLYlink written 12 weeks ago by Kevin Blighe41k

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 REPLYlink modified 12 weeks ago • written 12 weeks ago by english.server140
1

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 REPLYlink written 12 weeks ago by Kevin Blighe41k

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

ADD REPLYlink written 12 weeks ago by english.server140
1

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 REPLYlink written 12 weeks ago by Ahill1.5k

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

ADD REPLYlink modified 12 weeks ago • written 12 weeks ago by english.server140
1

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

ADD REPLYlink written 12 weeks ago by Benn6.6k

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

ADD REPLYlink written 12 weeks ago by english.server140

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

ADD REPLYlink written 12 weeks ago by english.server140
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1600 users visited in the last hour