Advanced Statistics - Biology 6030

Bowling Green State University, Fall 2017

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)
```

Competences earned this week:

  1. Relate multivariate distances to a grouping variable

last modified: 9/30/17
This material is copyrighted and MAY NOT be used for commercial purposes, 2001-2017 lobsterman.
[ Advanced Statistics Course page | About BIO 6030 | Announcements ]
[ Course syllabus | Exams & Grading | Glossary | Evaluations | Links ]