[BioC] RE: correcting for 3' bias in highly amplified RNA samples

Reimers, Mark (NIH/NCI) reimersm at mail.nih.gov
Thu Dec 2 15:40:44 CET 2004

Hello Ben,
Our collaborators have been taking microdissected samples and amplifying
them. We find that the distribution of probe intensities in a probe set is
greatly affected; the signal from 5' probes is much decreased. However if
the amplifications are done carefully, the amplified samples can be compared
to each other. We find the RNA degradation plots in affy a good way to
assess comparability. 
I don't think amplified samples could be compared with un-amplified samples,
if that was your aim.



Original Message:
Date: Wed, 1 Dec 2004 14:49:08 -0500 
From: "Wittner, Ben" <Wittner.Ben at mgh.harvard.edu>
Subject: [BioC] correcting for 3' bias in highly amplified RNA samples
	and	Affyme trix chips
To: "Bioconductor List (bioconductor at stat.math.ethz.ch)"
	<bioconductor at stat.math.ethz.ch>
	<C6B4E960236FD311B4E00008C7F406E31404B6F8 at phsexch11.mgh.harvard.edu>
Content-Type: text/plain

Is there some way in Bioconductor to correct for 3' bias in Highly amplified
RNA samples for Affymetrix chips.

I know that Affy now has a 3' biased human chip, but I have human data that
was done with another chip and cannot be re-done. I also have mouse data and
I don't think there is a 3' biased mouse chip from Affy.

I've heard of people doing such a correction (not necessarily using BioC or
R), but I can't find any mention of it in the affy documentation or in the
Bioconductor mailing list archives.



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