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


```r
library(RColorBrewer)
```


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



```r
# 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


```r
# 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 of chunk plotDensities](figure/plotDensities1.png) 

```r

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")
```

![plot of chunk plotDensities](figure/plotDensities2.png) 

```r
# dev.off()
```




## Appendix


```r
getwd()
```

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



```r
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
```