Question: Beginner Help with Microarray Analysis
gravatar for tareagan
2.5 years ago by
tareagan0 wrote:

Hi. I am an undergraduate working in a biology lab that studies arabidopsis guard cells. My mentor has assigned me with a project to write code that will take gene expression data from an affymetrix microarray chip and then interpret that into a meaningful graphical representation of gene expression values for the cells. My question is regarding the actual form of the data. I realize that microarrays return data in the form of what looks like colored grids of green and red. However, I am confused regarding the nature of "gene expression values". How is an expression value quantified? Understanding the nature of the data would assist greatly with my work as I am concerned with understanding what I am doing more so than blindly installing R's Bioconductor package and surviving off of web tutorials. Thank you for any help in explaining this process.

chip-seq R • 929 views
ADD COMMENTlink written 2.5 years ago by tareagan0

The way I see, installing R's Bioconductor package and surviving off of web tutorials will help you understand the data and the analyses - just don't do it "blindly". Also, check the limma user guide, it is very detailed and well-explained.

Regarding specific array platforms, you should seek information at the manufacturer site.

P.S.: not all microarrays are two-color, red-green arrays.

ADD REPLYlink written 2.5 years ago by h.mon29k

Thank you for the reply. I guess I was really just looking for a good place to start as all the references I have gone to over the past few days have described things as if I was already familiar with every mechanism. I'll be sure to follow your advice!

ADD REPLYlink written 2.5 years ago by tareagan0

There are several books that can walk you through the basics of microarrays and associated data analysis. You could take a look at your local institutional library.

ADD REPLYlink written 2.5 years ago by genomax76k

Read this and you will be enlightened:

ADD REPLYlink written 2.2 years ago by Kevin Blighe53k
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