[BioC] get over it/WAKE uP and SMELL the COFFEE

Ann Loraine loraine at loraine.net
Thu Dec 18 16:03:39 MET 2003

My apologies if this is off-topic.  If you like, feel free to respond  
directly rather than posting to the list.

Affymetrix made this announcement recently:


In a nutshell, they are announcing that they want to develop target  
preparation protocols that amplify the full length of target mRNAs with  
the ultimate goal of identifying splice variants.

Many splice variants (most notably variants of genes involved in  
apoptosis) produced by the same gene exhibit different, sometimes even  
antagonistic biological functions. An expression array that could  
reliably produce information about how splicing varies from cell type  
to cell type would certainly be useful.

Chad argues that focusing on individual genes using micro-array data is  
problematic.  Would a chip designed to measure the relative abundance  
of individual mRNAs produced by a single gene merely magnify these  
problems?  Are the statistics of microarray expression analysis  
'strong' enough to allow analysis of individual mRNAs from the same  

I would be very interested to learn what members of this list think  
about this development.


Ann Loraine

On Dec 18, 2003, at 6:09 AM, Stephen Henderson wrote:

> I agree with some of WHAT you say CHAD, the PROBLEM is THAT MOST
> multiVARIATE methods are BUILt on top OF the marginal tests. FOR  
> instance
> machine learning methods are based on gene subsets for each of k CROSS
> validations. USE of the appropriate TEST (fold/T/F/cyber-T/etc..)for  
> subset
> selection is IMHO the most IMPORTANT!! choice .
> Stephen
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