Setup SCDE in R engine
From Array Suite Wiki
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)
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:
- Run SCDE locally: OmicsoftHomeDirectory\RScripts by default.
- Run SCDE on server: BaseDirectory\Pipeline\RScripts by default.
This SCDE script can be downloaded from here.