Description Usage Format References Examples
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.
1 | data("yang_nl10")
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A data frame with 40683 observations on the following 3 variables.
CFP
a numeric vector
Venus
a numeric vector
mCherry
a numeric vector
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.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 | 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])
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