BIOL 210: Application and Analysis of (Biological) Microarrays

Final Project - Part II

Suggestions for your Analysis

Variable Growth Temperatures

Radiation Experiment

Pyrococcus furiosus print "A" GAL file
Pyrococcus furiosus gene description / annotation text file

Pyrococcus ORF sequences (FASTA sequence file)
Pyrococcus intergenic sequences (FASTA sequence file)

Use the X Cluster Program for clustering your data. Use the binaries I emailed you today (March 10). Alternatively, you can try a less buggy version of the Eisen cluster program here.

Improved R script (3/14) for converting normalized arrays in R to PCL format
After sourcing this file, you'll have a function "pclfile()" that takes three parameter: An marrayRaw/marrayNorm object, the resulting output filename (place in quotes), and a third, optional parameter that takes the filename of a gene description file. Save the P. furiosus gene description file above in your working directory, then pass it's name (Pfu-annote.txt) as the third parameter. Then Cluster & try in TreeView. You should now see gene descriptions (hopefully). Thanks again to Andy for the quick improvement to his code.