[BioC] Pointers on importing peptide (protein) expression data

Jamie Sherman jamie_bio at mac.com
Tue Apr 26 12:06:49 CEST 2005

I'm new to BioConductor and have given the faqs a read through as well 
as some of the tutorials but need someone to point me in the right 
direction because the data I have is a little unusual. I'll explain 
what I have and then what I would like to do.

What I have.
The data I have looks like this

Protein_Name  Peptide_Mass: T1 T2 T3 T4 T5 T6 T7

T[1-7]  is the expression ratio at time point [1-7] and is a ratio of 
abundances of the sample to a reference.

What I would like to do.

This data seems similar to what you might get out of an array 
experiment. I am wondering if I can load the data in a way that would 
allow me to make use of the annotation package to attach GO information 
and then use the applicable array analysis packages.

	Is BioConductor a suitable tool for this?
	What is the best way to load this data? (where should I be looking)

	Can you recommend  analysis packages to clustering by GO and to 
cluster on patters in the protein expression data?

Thanks for looking at this, I really appreciate it.

Jamie Sherman
Graduate Student
Genome Sciences, UW
Seattle, WA

  time course of protein expression data.

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