Setup tSNE in R engine

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Contents

setup SCDE

Overview

This wiki demonstrates user how to setup tSNE in R engine, so user can run R-tSNE in ArrayStudio GUI. We have designed the tSNE GUI for user to input/modify the tSNE parameters, when user send the job to run, the actual job is run by the R engine in their local machine or the R engine on their server, with the parameters parsed from the GUI. And when the job is finished in R, ArrayStudio will import the results back to the project file, and user can have customized visualization with the result in ArrayStudio GUI.

Install Rtsne in R

Before user check the R engine on ArrayStudio, they should install Rtsne packages in their REngine Excutable Path integrated with ArrayStudio.

Run this commend in R to install package "Rtsne":

install.packages("Rtsne")

For local analysis, user can check the REngine Excutable Path like this:

SetupRtsne01.png

SetupRtsne02.png

For server analysis, user (only admin person) can check the REngine Excutable Path like this:

SetupRtsne03.png

SetupRtsne04.png

Download Rtsne scripts

Now Rtsne can be run successfully in R. In order to run Rtsne through ArrayStudio, we need to download a text file containing the Rtsne script, and put this file into the RScript folder.

RScript folder can be found accordingly for local runs or server runs:

Instead of manually downloading this Rtsne script, user can easily finish this by GUI:

SetupRtsne02.png

Check the option for Install/Update for rtsne ScriptName, and click Update. Then the Rtsne script will be automatically downloaded to the RScript folder. Admin person can do the same for server.

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