Pre-processing features (genes): Raw Arabidopsis data

Last updated: 2018-08-20

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library(Biobase)
library(limma)

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

plotDensities(eset, legend = FALSE)

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

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

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

# 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)

sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17134)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
[1] limma_3.36.1        Biobase_2.40.0      BiocGenerics_0.26.0

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1   Rcpp_0.12.17      digest_0.6.15    
 [4] rprojroot_1.3-2   R.methodsS3_1.7.1 backports_1.1.2  
 [7] git2r_0.21.0      magrittr_1.5      evaluate_0.10.1  
[10] stringi_1.2.3     whisker_0.3-2     R.oo_1.22.0      
[13] R.utils_2.6.0     rmarkdown_1.10    tools_3.5.0      
[16] stringr_1.3.1     yaml_2.1.19       compiler_3.5.0   
[19] htmltools_0.3.6   knitr_1.20       

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