[BioC] Affymetrix is changing its labelling kit - data analysiswill change!?

[Francois Collin]

"nice separation with PM significantly higher than MM" - that might make the
MMs more attractive as candidate controls to correct for cross
hybridization, but the real question is whether the resulting corrected PM
intensity is proportional to target transcript abundance?
This is not automatic.  When comparing different ways to isolate RNA from
whole blood, for example, we see that the different protocols lead to clear
differences in % present calls (i.e. PM significantly higher than MM), but
it is not clear whether these differences translate into better measurements
of  expression (we are conducting an experiment to assess this).  Is there
any indication that the new labelling kit will lead to better overlall data,
or is the change primarily intended to make the PM-MM measures more
attractive?

-francois



----- Original Message ----- 
From: "Matthew Hannah" <Hannah at mpimp-golm.mpg.de>
To: <bioconductor at stat.math.ethz.ch>
Sent: Wednesday, September 08, 2004 9:26 AM
Subject: [BioC] Affymetrix is changing its labelling kit - data analysiswill
change!?


> Hi,
>
> I thought I'd post this here, something to think about, especially if data
from the latest chips lands on your desk.
>
> Had a seminar today from the affy rep - they are changing labelling
kit/procedure from ENZO to IVT. The new one is better BUT you will not be
able to directly compare between new and old. You will still be able to buy
direct from ENZO to complete current projects.
>
> The biggest change appears to be they will switch to just using
biotin-pseudouridine instead of biotin U and C. There are details below, but
I can't find the really interesting figure he showed - which was a
comparison of the PM and MM signals (of the spike-ins I guess) with ENZO
(big overlap - as we know!) and with IVT (nice separation with PM
significantly higher than MM). This will probably have a big impact on
computing expression and detection.
>
> Something to keep us on our toes...
>
> http://www.affymetrix.com/support/technical/technotes/ivt_technote.pdf
>
> Also, better order the new computer as there could be alot of data - they
are already down to 11µm from the previous 18µm, 5µm is on the way, and
there is rumour of 1-2µm...
>
> Cheers,
> Matt
>
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