VST transformation

Loading the R environment

library("DESeq")
library(reshape)
library(ggplot2)

Reading input

filename = "counttable1.tsv"
raw_counts = read.csv(filename, sep = "\t", header = T, row.names = 1, stringsAsFactors = F)
raw_counts_deseqct = newCountDataSet(raw_counts[, c(1, 2)], factor(c("can", 
    "can")))

Performing VST transformation

raw_counts_deseqct = newCountDataSet(raw_counts[, c(1, 2)], factor(c("can", 
    "can")))
raw_counts_deseqct = estimateSizeFactors(raw_counts_deseqct)
raw_counts_deseqctBlind = estimateDispersions(raw_counts_deseqct, method = "blind")
vsd = varianceStabilizingTransformation(raw_counts_deseqctBlind)
vst_raw_counts = exprs(vsd)

write.table(vst_raw_counts, file = "vst_transf_tabout.txt", sep = "\t", quote = F, 
    col.names = NA, row.names = TRUE)
head(vst_raw_counts)

##              can_1  can_2
## FBgn0000003 10.095 10.155
## FBgn0000008 11.078 11.130
## FBgn0000014  9.834  9.921
## FBgn0000015  9.834  9.834
## FBgn0000017 12.450 12.406
## FBgn0000018 10.414 10.429

vst_raw_counts_melted = melt(vst_raw_counts)
ggplot(data = vst_raw_counts_melted, aes(value, colour = X2))

## Error: No layers in plot

+geom_density(alpha = 0.2)

## Error: invalid argument to unary operator

+labs(x = "VST of counts")

## Error: invalid argument to unary operator

for (sample in colnames(vst_raw_counts)) {
    hist(vst_raw_counts[, colnames(vst_raw_counts) == sample], main = paste("Sample", 
        sample), breaks = 80, xlab = "VST counts")
}

Logging R environment

sessionInfo()

## R version 3.0.1 (2013-05-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## 
## 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=C                 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] ggplot2_0.9.3.1    reshape_0.8.4      plyr_1.8          
##  [4] DESeq_1.12.0       lattice_0.20-15    locfit_1.5-9.1    
##  [7] Biobase_2.20.1     BiocGenerics_0.6.0 markdown_0.6.1    
## [10] knitr_1.2         
## 
## loaded via a namespace (and not attached):
##  [1] annotate_1.38.0      AnnotationDbi_1.22.6 colorspace_1.2-2    
##  [4] DBI_0.2-7            dichromat_2.0-0      digest_0.6.3        
##  [7] evaluate_0.4.4       formatR_0.8          genefilter_1.42.0   
## [10] geneplotter_1.38.0   grid_3.0.1           gtable_0.1.2        
## [13] IRanges_1.18.2       labeling_0.2         MASS_7.3-27         
## [16] munsell_0.4.2        proto_0.3-10         RColorBrewer_1.0-5  
## [19] reshape2_1.2.2       RSQLite_0.11.4       scales_0.2.3        
## [22] splines_3.0.1        stats4_3.0.1         stringr_0.6.2       
## [25] survival_2.37-4      tools_3.0.1          XML_3.98-1.1        
## [28] xtable_1.7-1