Help with analyzing microarray data - absolute beginner!!

Question

[krishnakarthik.vemuri]

Hi,

I am an absolute novice at analyzing microarray data. I recently was able to persuade a research to let me analyze some microarray data for him. He sent me the data as an Excel file, and gave me the following description of the data:

• Both files have the data. One is a txt file and the other is in xls. The Agilent array platform was used for this data with a 2-color fluorescence. Thus, the data are reported as a ratio of the 2 colors representing unirradiated controls vs irradiated.
• It would probably be best if you do paired t-tests to create a list of the genes and fold-changes for me to look at. Heat maps would probably be the simplest visualization.
• Then run the data through MeV to control the false discovery rate. I think the default is usually 0.80. Then get the heat map of this set.

The Excel file has a column labelled as AGI_HUM1_OLIGO_A_23_P100001, which I am sure are probes for individual genes.

My problem is, I am not sure I can do it with the data given. Don't I need the .gpr files in order to read the data into R using the limma package? And where can I get the annotation data to identify the genes from the probes?

If someone could give some basic directions to using the mev software, like what inputs to use and whether or not annotations should be used with the data and where to get them, I would be really grateful.

Thanks a lot for any help I can get here!

Answer 1

[pld]

All of the annotation files required are available from Agilent. For R, you only need the GAL file to use limma with your data, which again you can get from Agilent. After that, follow the limma documentation, which is fairly through for performing two color analysis.

The only major difference in the documentation between the Affymetrix examples used and the Agilent data you're using is the stage where you pull the data into R. After that you should be good.