Last updated: 2019-02-26

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Knit directory: dc-bioc-limma/analysis/

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Untracked files:
    Untracked:  analysis/table-s1.txt
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File Version Author Date Message
html 2372aa1 John Blischak 2019-01-09 Build site.
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
2372aa1 John Blischak 2019-01-09
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
2372aa1 John Blischak 2019-01-09
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
2372aa1 John Blischak 2019-01-09
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
2372aa1 John Blischak 2019-01-09
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
2372aa1 John Blischak 2019-01-09
f440a87 John Blischak 2018-08-20
eafed69 John Blischak 2018-08-09 


sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3

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_3.38.3        Biobase_2.42.0      BiocGenerics_0.28.0

loaded via a namespace (and not attached):
 [1] workflowr_1.2.0.9000 Rcpp_1.0.0           digest_0.6.18       
 [4] rprojroot_1.2        backports_1.1.3      git2r_0.24.0        
 [7] magrittr_1.5         evaluate_0.13        stringi_1.3.1       
[10] fs_1.2.6             whisker_0.3-2        rmarkdown_1.11      
[13] tools_3.5.2          stringr_1.4.0        glue_1.3.0          
[16] xfun_0.5             yaml_2.2.0           compiler_3.5.2      
[19] htmltools_0.3.6      knitr_1.21