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

[Wittner, Ben]

Thanks Mark. I think all your comments below are right. Nevertheless, I expect
that the signal to noise ratio would be improved by de-emphasizing the results
from the probes at the 5' end because presumably their signal-to-noise is worse
than that of the probes at the 3' end. -Ben

Date: Thu, 2 Dec 2004 09:40:44 -0500 
From: "Reimers, Mark (NIH/NCI)" <reimersm at mail.nih.gov>
Subject: [BioC] RE: correcting for 3' bias in highly amplified RNA
	samples
To: "'bioconductor at stat.math.ethz.ch'"
	<bioconductor at stat.math.ethz.ch>
Message-ID:
	<16A0583FB1644E4DB8C0A0265028B6FD9306EB at nihexchange13.nih.gov>
Content-Type: text/plain

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.

Regards

Mark

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>
Message-ID:
	<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.

Thanks.

-Ben