maSigPro package R, time course analysis, clustering

Member for

2 years Mrs_Sippi

Hi,

I have a more or less general question. 

Has anyone experience with time course analysis (+ clustering) based on (normalized) count data with Knime or may give me a short estimation if coding in R within Knime is a useful approach? 

Until now I worked with R and the MaSigPro package, but R is a little bit extensive in some cases. I would like to simplify some basic steps like the preparation of the data sheets with Knime and it would be nice to combine the preparation and the analysis in R in one workflow.

Unfortunately, I didn't find much about this topic in the forum, but maybe someone has already gained experience in this topic and can give me suggestion about my plans?! 

Comments
Thu, 08/17/2017 - 12:33

Member for

10 months 1 week

RolandBurger

Hi Mrs_Sippi,

This should not be a problem. If you can do all the necessary data prep steps in KNIME, you can then use an R Snippet node to pass the data to R. Afterwards, the results are send back to KNIME.

Please see here for an example how to use R from within KNIME: https://www.knime.com/nodeguide/scripting/r/example-of-r-snippet

Cheers,

Roland