Setup SCDE in R engine

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setup SCDE

Overview

This wiki demonstrates user how to setup SCDE in R engine. Unlike the DESeq package, which has been implemented in ArrayStudio code, SCDE needs to be run with R scripts, through packages installed in ArrayStudio. Before user check the R engine on ArrayStudio, they should install SCDE packages in their R (the R path they defined in R engine executable path)


Install SCDE in R

Currently, the default installation of SCDE will have issue running in R since this error when build error model:

error info: Error in FUN(Xi, ...) :
trying to get slot "logLik" from an object of a basic class ("function") with no slots

This is resulted from a new version of package flexmix, we can install a previous version of flexmix to avoid this:

install.packages("devtools")  # this command install devtools first if you don’t have devtools installed
require(devtools)
install_version("flexmix", version = "2.3-13", repos = "http://cran.us.r-project.org")

Then we can get a specific version of SCDE and recompile:

require(devtools)
devtools::install_github('hms-dbmi/scde', build_vignettes = FALSE)

The following combination works fine in R (windows)

scde_1.99.4     flexmix_2.3-13

Download SCDE R scripts

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

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

This SCDE script can be downloaded from here.

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