yang_nl10: Expression of reporter genes in the NL010 E. coli cells from...

In noise: Estimation of Intrinsic and Extrinsic Noise from Single-Cell Data

Expression of reporter genes in the NL010 E. coli cells from Yang et al (2014).

Description

Expression of reporter genes CFP and mCherry in over 40,000 E. coli cells. A subset of these values are displayed in a scatterplot in Yang et al (2014) Fig 3a rightmost panel.

Usage

data("yang_nl10")

Format

A data frame with 40683 observations on the following 3 variables.

CFP

a numeric vector

Venus

a numeric vector

mCherry

a numeric vector

References

Yang, S., S. Kim, Y. R. Lim, C. Kim, H. J. An, J.-H. Kim, J. Sung, and N. K. Lee (2014) Contribution of RNA polymerase concentration variation to protein expression noise. Nature Communications, 5, 4761.

Examples

data(yang_nl10)

# compute the noise estimates

# no normalization
# unscaled by mean
unlist (computeIntrinsicNoise (yang_nl10[,1], yang_nl10[,3]))
unlist (computeExtrinsicNoise (yang_nl10[,1], yang_nl10[,3]))

# scaled by mean
unlist (computeIntrinsicNoise (yang_nl10[,1], yang_nl10[,3])) / 
    mean (yang_nl10[,1]) / mean(yang_nl10[,3])
unlist (computeExtrinsicNoise (yang_nl10[,1], yang_nl10[,3])) / 
    mean (yang_nl10[,1]) / mean(yang_nl10[,3])

# quantile normalization on log2 transformed data
# install bioconductor package for quantile normalization
# source('http://bioconductor.org/biocLite.R')
# biocLite('preprocessCore')
library(preprocessCore)

# ignore a few values that are negative
yang_nl10.pos <- yang_nl10[-which (yang_nl10[,1]<0),]
yang_nl10.pos.log2.quant <- normalize.quantiles (as.matrix (log2 (yang_nl10.pos[,c(1,3)])))

# unscaled by mean
unlist (computeIntrinsicNoise (yang_nl10.pos.log2.quant[,1], yang_nl10.pos.log2.quant[,2]))
unlist (computeExtrinsicNoise (yang_nl10.pos.log2.quant[,1], yang_nl10.pos.log2.quant[,2]))

# scaled by mean
unlist (computeIntrinsicNoise (yang_nl10.pos.log2.quant[,1], yang_nl10.pos.log2.quant[,2])) / 
    mean (yang_nl10.pos.log2.quant[,1]) / mean(yang_nl10.pos.log2.quant[,2])
unlist (computeExtrinsicNoise (yang_nl10.pos.log2.quant[,1], yang_nl10.pos.log2.quant[,2])) / 
    mean (yang_nl10.pos.log2.quant[,1]) / mean(yang_nl10.pos.log2.quant[,2])

noise documentation built on May 29, 2024, 2:08 a.m.