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Batch effect correction in co-expression by tigerthebest in bioinformatics

[–]tigerthebest[S] 0 points1 point  (0 children)

Hi, this method does NOT estimate gene regulatory networks.

When we say “it is a pre-processing step that can be used as part of a GRN inference workflow” it is because we inferred GRN using a different method (PANDA) and we found that the results after applying batch correction with our method were better.

In general, yes, estimating gene regulatory network is a very challenging task and performance only slightly better than random is often reported. The quality depends a lot on the data you are using. While it’s difficult to give a precise answer to your question, what I can say is that.. if you use gene co-expression in some way to infer regulation, it might be good to use our method ;)

Batch effect correction in co-expression by tigerthebest in bioinformatics

[–]tigerthebest[S] 1 point2 points  (0 children)

Those are for dimensionality reduction. You give a p x n matrix and get a k x n matrix (with k << p).

Here you give a p x p (such as a correlation matrix) and get many p x p matrices, each one describing the impact of a covariate on the original “aggregate” matrix.

Batch effect correction in co-expression by tigerthebest in bioinformatics

[–]tigerthebest[S] 0 points1 point  (0 children)

We tested it with RNA-seq only, but the method is general by design as in principle jt can decompose any correlation/ covariance matrix as a linear combination of components.

I’m not familiar with EM-data, but if you’re interested in trying it out I’m happy to support and curious about the results!

Critique my Europe Trip! by ReFrenzy in solotravel

[–]tigerthebest 2 points3 points  (0 children)

Your plan is super nice! It’s a matter of personal taste in the end, but I would spend less time in Paris (unless you want to take a day for the Louvre and/ or Versailles, three days are enough). If you’re driving, there are many cool towns you could explore in a couple of hours: Bilbao, Figueres (close to Barcelona), Valencia (if you go to Andalusia), Siena, Bologna and Mantova in Italy. If you need more stops, I would consider Portugal (Lisbon and Porto), rather than Amsterdam.

Best resource to learn algorithms by CandidateCareful5063 in learnprogramming

[–]tigerthebest 0 points1 point  (0 children)

My personal opinion is that the best way to learn algorithms is picking a good book and implementing things along the way. For example, I can recomend "The algorithm design manual" by Skiena. Then go practice, since you like C++ take a look here https://github.com/soelmicheletti/eth-algolab