Benchmark ArrayStudio to RStudio.pdf

From Array Suite Wiki

Jump to: navigation, search


Contents

Overview

SCDE (Single Cell Differentiate Expression) is a R package implements a set of statistical methods for analyzing single-cell RNA-seq data. Here we used SCDE R package version 1.99.4 and flexmix version 2.3.13.The outputs from ArrayStudio and RStuido are compared, a scatter plot is shown below.

Dataset

We used the same datasets used in the SCDE package demo dataset (es.mef.small),14897 genes and 40 samples (ESC vs MEF).

Comparision between SCDE results from RStudio and ArrayStudio

SCDE R AS.png

Benchmark note

Both SCDE module in ArrayStudio and SCDE package in RStudio gave identical estimates and p-values.