Pre-processing features (genes): Raw Arabidopsis data

Last updated: 2018-08-09

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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 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] limma_3.32.2        Biobase_2.36.2      BiocGenerics_0.22.1

loaded via a namespace (and not attached):
 [1] workflowr_1.1.1.9000 Rcpp_0.12.18         digest_0.6.15       
 [4] rprojroot_1.3-2      R.methodsS3_1.7.1    backports_1.1.2-9000
 [7] git2r_0.23.0         magrittr_1.5         evaluate_0.11       
[10] stringi_1.2.4        whisker_0.3-2        R.oo_1.22.0         
[13] R.utils_2.6.0        rmarkdown_1.10       tools_3.4.4         
[16] stringr_1.3.1        yaml_2.2.0           compiler_3.4.4      
[19] htmltools_0.3.6      knitr_1.20          

This reproducible R Markdown analysis was created with workflowr 1.1.1.9000