Residual Disease Paper

Comparing Ovary and Omentum Expression

by Shelley Herbrich

May 13, 2013

1 Executive Summary

1.1 Introduction

In this report, we compare the PCR expression of our target genes between ovary and omental samples.

1.2 Data & Methods

Here, we use PCR quantification summaries of samples run on the 17 plates containing tissue from both ovary and omentum.

1.3 Results

We produce density plots of ADH1B and FABP4 expression by tissue.

We see that for both genes, omental levels are markedly higher than ovary.

2 Loading PCR Data

library(RColorBrewer)

load(file.path("RDataObjects", "OMResults.RData"))
load(file.path("RDataObjects", "PCRResults.RData"))

# match plates
plate <- unique(OMResults$Plate)
ovFABP4 <- PCRResults$FABP4[which(PCRResults$Plate %in% plate)]
ovADH1B <- PCRResults$ADH1B[which(PCRResults$Plate %in% plate)]

3 Plotting Densities of ADH1B and FABP4 Expression

# pdf(file='OVOMExpression.pdf',paper='USr')
plot(density(ovADH1B), col = "red", xlim = c(-30, -5), main = "ADH1B Expression")
lines(density(OMResults$ADH1B), col = "grey")
legend("topright", c("Ovary", "Omentum"), col = c("red", "grey"), lty = 1, bty = "n")

plot(density(ovFABP4), col = "red", xlim = c(-30, -5), main = "FABP4 Expression")
lines(density(OMResults$FABP4), col = "grey")
legend("topright", c("Ovary", "Omentum"), col = c("red", "grey"), lty = 1, bty = "n")

# dev.off()

Appendix

getwd()

## [1] "\\\\mdadqsfs02/workspace/kabagg/RDPaper/Webpage/ResidualDisease"

sessionInfo()

## R version 2.15.3 (2013-03-01)
## Platform: x86_64-w64-mingw32/x64 (64-bit)
## 
## 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] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
## [1] RColorBrewer_1.0-5 knitr_1.2         
## 
## loaded via a namespace (and not attached):
## [1] digest_0.6.3   evaluate_0.4.3 formatR_0.7    stringr_0.6.2 
## [5] tools_2.15.3