Newbie question about microarray analysis

Austin P. So (Hae-Jin) nobody at nowhere.com
Mon May 29 12:09:59 EST 2006


Rex Eastbourne wrote:
> Thank you, Austin! Very helpful.
> 
> I've got a better description of what I need to do now. I have a
> collection of proteins in a spreadsheet, and need to find out:
> 
> -Are some of them related to one another?
> -Do they participate in a single transduction pathway in the cell or
> between cells?
> 
> Does this sound like a hard task for someone with lots of math but no
> bio?

Hi Rex...

If it is a matter of "relationship" (in the sense that a set of proteins 
behave i.e. go up or down in the same way over a given treatment), then 
any k-means algorithm will do the trick. I'm pretty sure this would be a 
no-brainer for you. I'm actually surprised they don't give it a go by 
themselves...

Anything else (like your second point...though I'm curious about the 
experimental design) you'd have to give more details, say:

col1=proteinID
col2=expt1
col3=expt2
etc...

BTW...If you don't want to do it, then don't. Technically, if the person 
is doing a PhD, then he/she should know how to do it themselves anyway 
and not just hand it off...

Austin


P.S. what is your math background? I should have probably asked that 
first...


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