Wednesday, April 18, 2018

PRESTO! Collect all sorts of data and let MatLab sort it out.

EDIT 4/24/18: If you don't have MatLab there is a PRESTO stand-alone! You can find it here. 

I can clearly remember my excitement when I first saw 2 different "-omics" datasets integrated together (that totally worked) in a great study. It might still be in the 1,000+ entries on this scrambled blog, but who will ever know (the search bar appears to lose power as the entries get older -- which is honestly fine by me, I've said some dumb stuff over the years)

These days -- I'm still impressed -- but it's a lot more common. However, I haven't pulled one off myself yet but I'd sure love to....but where do you even start....what about here?

First impression -- wow -- this looks seriously powerful. This team pulls in a bunch of different datasets -- microarrays, proteomics, my heart jumped for just a second because I thought they were also integrating CyTOF data (I don't think they do here, they just discuss the statistics involved) and through "t-stochastic neighbor embedding" --


-- they massively reduce a staggering amount of signals from various sets to very small and shockingly meaningful observations.

Is it a trick?

Honestly, I can't say for sure, but the results seem logical and really impressive. (Two gifs is probably too much for one post).

I start to get nervous as soon as we start talking statistics things -- but if it gets you to a small number of targets that you can validate (and they do) it's a WIN.

I made sure to mention MatLab in the title of this post. MatLab is not free software (though trials are available and many many University's have license deals for the software). There is also a home version that is roughly 1/10 the normal license price, but has some limits on it's functionality. If you have access to this software --- and have some huge and intimidating "omics" data sets you should definitely check this out!

EDIT: I accidentally reread this and I feel like I didn't emphasize this study correctly. PRESTO is a utility that these authors developed that runs in/on MATLAB. I don't mean the title of this post (which -- to some extent -- can't be changed now) to detract from the awesome amount of work PRESTO is.

1 comment:

  1. Thank you so much for the signal boost! I just wanted to let you know that there is a compiled version of the software that doesn't require a Matlab license. Any one can use it, and the executable can be found here:

    Also, I love the gifs.

    Sara McArdle