[BioC] Chip Analysis Assistance

[Luckey, John]

Hello,

My name is John Luckey. I am a post-doctoral researcher in Diane Mathis and Christophe Benoist's lab in the Joslin Diabetes Center and am currently analysing many different chip experiments in hopes of identifying genes differentially expressed in various T-cell subsets. I have been working within S-plus so far. I have just discovered the bioconductor site and am currently going through the available support online. In reading the literature, searching the web for available resources, and working through our own data, I am quite interested in trying out the R-based resources. 

In a more general sense, I am also looking for someone with more expertise than my own (shouldn't be hard to find) in the area of chip analysis who might be willing to talk through my analysis issues over a coffee or drink of their choice. I am particularly interested in affy probe level analysis, "prefiltering" data based on variance, normalization methods, and estimates of false positives rates. ( Since my goals are identification of candidate genes to further test via other methods, I am ultimately interested in minimizing my false positive rates). In addition, I have a strong interest in applying affy chip analysis towards time courses,  and in particular, dose respose course, data sets. Any assistance would be greatly appreciated.

Sincerely,
John Luckey


C John Luckey, MD PhD
Post Doctoral Fellow  - Mathis- Benoist Lab
Joslin Diabetes Center
One Joslin Place, Rm. 474
Boston, MA  02215
phone: (617) 264-2783
fax:     (617) 264-2744
e-mail: john.luckey at joslin.harvard.edu