Labs for Advanced Stats

Expression Data II - Lab Exercises

This lab analyzes gene expression data from a breast cancer study. There are 24 samples with 12625 expression measures. Here is a way to read the data in.

```{r data}
#source("https://bioconductor.org/biocLite.R")
#biocLite()
if (!require("Biobase")) install.packages("Biobase")
library(Biobase)
#download.file("ftp://ftp.umiacs.umd.edu/pub/hcorrada/chang03.rda", destfile="./chang03.rda")
load("chang03.rda")
show(chang03)
```

I'd recommend doing a couple of things before you get too deeply into it ...

```{r data frame}
descrDF = pData(chang03)
names(descrDF)
table(descrDF$disease.state,descrDF$Progesterone..receptor.status)
exprDF = exprs(chang03)
dim(exprDF)
summary(exprDF)
boxplot(exprs(chang03))
exprDF_log <- log2(exprDF)
```

I trust you have made friends with the data last week
Identify those genes whose expression best distinguishes cancer samples that were resistant or sensitive to the chemotherapy

Competences earned this week:

Relate multivariate distances to a grouping variable

last modified: 9/30/17