New publication

Posted Leave a commentPosted in Publication

The November issue of Computer Methods and Programs in Biomedicine
contains an article about my R-package ‘GenomicTools’:

http://www.sciencedirect.com/science/article/pii/S0169260716308549

 

The R-package GenomicTools for multifactor dimensionality reduction and the analysis of (exploratory) Quantitative Trait Loci

Background and objectives

We introduce the R-package GenomicTools to perform, among others, a Multifactor Dimensionality Reduction (MDR) for the identification of SNP-SNP interactions. The package further provides a new class of tests for an (exploratory) Quantitative Trait Loci analysis that overcomes some of the limitations of other popular (e)QTL approaches. Popular (e)QTL approaches that use linear models or ANOVA are often based on over-simplified models that have weak statistical properties and which are not robust against outlying observations.

Method

The algorithm to calculate the MDR is well established. To speed up its calculation in R, we implemented it in C++. Further, our implementation also supports the combination of several MDR results to an MDR ensemble classifier. The (e)QTL test procedure is based on a generalized Mann-Whitney test that is tailored for directional alternatives, as they are present in an (e)QTL analysis.

Results

Our package GenomicTools provides functions to determine SNP combinations that have the highest accuracy for a MDR classification problem. It also provides functions to combine the best MDR results to a joined ensemble classifier for improved classification results. Further, the (e)QTL analysis is based on a solid statistical theory. In addition, informative visualizations of the results are provided.

Conclusion

The here presented new class of tests and methods have an easy to apply syntax, so that also researchers inexperienced in R are able to apply our proposed methods and implementations. The package creates publication ready Figures and hence could be a valuable tool for genomic data analysis.

Exactly my type of humor

Posted Leave a commentPosted in News

In Germany abortions are illegal, but are not prosecuted, if they are performed within the first 12 pregnancy weeks and after the woman went to two(?!) consulting meetings. One thing that is, however, prosecuted is when a doctor advertises his or her service for abortion, especially if they have any financial interest or such. 

There was now a doctor in Germany who wrote on her webpage, that she performs abortions amd for an initiative called ‘Nie wieder!’ that was enough to suit her for violation of that paragraph 219a. The reason for doing so is, that the doctor shouldn’t advertise her service. The story becomes funny, when one notices that the head of that ‘Nie Wieder!’ association runs a webpage called www.abtreiber.com , where he lists some kind of ‘list of shame’ of doctors in Germany who perform or did perform abortions. In other words, they have a much more complete list of people whom to contact for an abortion than anybody else and they even do that PUBLIC!

So what do those guys want?! They suit individuals for advertising a service (that should be removed in their opinion), but offer at the same time a complete list of people who also offer that service. Seriously, what is the rational behind some peoples doing?!

Source: https://www.taz.de/Archiv-Suche/!5444891/

It has been a while

Posted Leave a commentPosted in Life

Today I realized, it has been a while that I added any content to this page, my apologies for that. It has been some kind of a summer… Lot of things happened, that kept me from writing things here, but I hope now things are getting more regular again.

I started today to improve the Recipe section on the page, I think it will be now much more convenient to navigate through the different recipes, I also continued to add more recipes to the page.

This guy certainly needs more recognition

Posted Leave a commentPosted in Music

For me it is difficult to understand that Jay Munly and his bands do not have more recognition, they are bloody awesome! It’s not too long ago that I found some songs on YouTube and they certainly are brilliant to listen! They nicely differ from the same jingles one hear here and there and they have great lyrics. Just to start with, check this one out and then I recommend to stroll through other songs from him and his band.
To my surprise he published even on Alternative Tentacles, hence I thought I would have found the records already earlier…

An Tagen wie diesen wünscht man sich eisgekühlten Bommerlunder!

Posted Leave a commentPosted in Life

Punk-Rock Millionär reagiert gereizt auf Systemkritik! Das die Toten Hosen seit einiger Zeit im Kuschelrock angekommen sind steht ja nun ausser Frage (ich behaupte einfach mal, dass deren Songs mittlerweile öfter auf WDR2 anstatt Radio Rock laufen…), aber dass Campino so dünnhäutig auf Kritik an anderen Pop-Song Textern reagiert, ist schon etwas überraschend… Da kritisiert Jan Böhmermann im Vorfeld der Echo Verleihung, dass in der deutschen Pop-Musik nur inhaltslose Phrasen zu Schunkelmusik gesungen werden und produziert einen Song, der (mehr oder weniger…) von Affen getextet worden ist und Campino hat während seiner Laudatio nichts besseres zu tun, als die Musikindustrie in Schutz zu nehmen.
Campino quatschte dabei vom ‘Böhmermannsche Zeitgeistgeplapper’ (was soll das sein?!) und meint ‘Lieber uncool sein als ein cooles Arschloch, das sich nicht konstruktiv einbringen kann’. Als ich noch jünger war, hatte ich Campino für ‘nur’ cool gehalten, jetzt muss ich sagen, uncool ist er immer noch nicht… Klar, ich kann verstehen, dass man die Leute, die einem eine Bühne geben in Schutz nehmen muss, aber ich hätte erwartet, dass der Böhmermann Kritik und die Einstellung der Toten Hosen hier eigentlich ähnlich sein würden?! Wobei, wenn ich mir so den Song ‘Unter den Wolken’ anhöre, da fehlt mir ein konstruktiver Ansatz, also alles weiterhin cool bei den Hosen.

Das widerlichste ist allerdings, dass die ‘Toten Hosen’ auf einer Veranstaltung spielten, bei der u.a. die ‘Böhsen Onkelz’ und ‘Frei.Wild’ zu den Nominierten in der Kategorie ‘Rock national’ gehörten! Erst auf einer Anti-Pegida-Demo spielen, dann aber mit dem Soundtrack von Pegida gemeinsam abfeiern und auf Kritik an der Veranstaltung dünnhäutig reagieren. Unfassbar wie gierig man werden kann, man sollte doch meinen, dass die Hosen schon genug gescheffelt hätten, um sich nicht mehr derart anbiedern zu müssen!