Last updated: 2019-01-09

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File Version Author Date Message
html f440a87 John Blischak 2018-08-20 Build site.
html eafed69 John Blischak 2018-08-09 Build site.
Rmd 75f3f79 John Blischak 2018-08-09 Organize analysis of pre-processing raw Arabidopsis data.

Setup

library(Biobase)
library(limma)
rds <- "../data/arabidopsis-eset-raw.rds"
eset <- readRDS(rds)

Visualize

plotDensities(eset, legend = FALSE)

Version Author Date
f440a87 John Blischak 2018-08-20
eafed69 John Blischak 2018-08-09

Log transform

exprs(eset) <- log(exprs(eset))
plotDensities(eset, legend = FALSE)

Version Author Date
f440a87 John Blischak 2018-08-20
eafed69 John Blischak 2018-08-09

Quantile normalize

exprs(eset) <- normalizeBetweenArrays(exprs(eset))
plotDensities(eset, legend = FALSE)

Version Author Date
f440a87 John Blischak 2018-08-20
eafed69 John Blischak 2018-08-09

Filter

# View the normalized gene expression levels
plotDensities(eset, legend = FALSE)
abline(v = 5)

Version Author Date
f440a87 John Blischak 2018-08-20
eafed69 John Blischak 2018-08-09 
# Determine the genes with mean expression level greater than 5
keep <- rowMeans(exprs(eset)) > 5
sum(keep)
[1] 12036
# Filter the genes
eset <- eset[keep, ]
plotDensities(eset, legend = FALSE)

Version Author Date
f440a87 John Blischak 2018-08-20
eafed69 John Blischak 2018-08-09 

sessionInfo()
R version 3.3.3 (2017-03-06)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] limma_3.30.13       Biobase_2.34.0      BiocGenerics_0.20.0

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1.9001 Rcpp_1.0.0           digest_0.6.13       
 [4] rprojroot_1.3-2      backports_1.1.2      git2r_0.23.0        
 [7] magrittr_1.5         evaluate_0.10.1      stringi_1.2.3       
[10] fs_1.2.6             whisker_0.3-2        rmarkdown_1.10.14   
[13] htmldeps_0.1.1       tools_3.3.3          stringr_1.3.1       
[16] glue_1.2.0.9000      yaml_2.2.0           htmltools_0.3.6     
[19] knitr_1.20