Application and Analysis of Microarrays
BME 210, Winter 2004

Lab 2: Bioconductor & normalization

 

 

Objective

 

Become familiar enough with R and Bioconductor to be able to perform normalization on your own.

 

I. Get the data

 

Surf over to the Bioconductor web home and take a quick look around at the resources available. From here, you get help downloading bioconductor at home/in your lab, there are multiple tutorials, and of course the software "packages" themselves.

After browsing around a bit, click on the left-hand panel option "Lab Materials". The "marray" package is what we will be primarily using for our analysis, so click on the ".pdf" link for cDNA Demo, and get started with this nice introduction to the package. Katie Pollard is a co-author on several modules in Bioconductor, so she is an expert -- please ask her questions.

Fire up "R" using the link from the same "class" folder you used to start up GenePix last week. Work through the examples in the tutorial. In the last half-hour of class, we will load up the data you gridded from last week, and you can get started analyzing it using the same tools demo'ed with the "swirl" dataset.

Note: The technical problem in the Kresge lab has been fixed -- you can use the computers there now for Bioconductor.

The two files you will need to load your own data into Bioconductor are:

 

Many thanks to Katie for making these files!!

Now, modify the two files above to work with the array you gridded last week (and save them with new names!).
Load them into a new working directory (i.e. on your desktop or in your CATS directory), and copy the .gpr and .gal files you created/used last week. If everything goes well, you should be ready to analyze now!

Here are a series of GPR result files from arrays I want you to analyze that will show good/bad/different qualities of hybs:

 

 

 

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