[BioC] Probe-level rma vs. gene-level rma in "Affy"

Skewes,Aaron ASkewes at mdanderson.org
Mon Jan 12 20:53:08 CET 2009

Actually, I am a bit confused by this too. I am attempting to reconstruct the protocol that Broad Institute uses for Copy number analysis. They told me that level 2 data is Probe-level RMA and level 3 data is gene-level RMA. What I think they really do is as follows:

Level 2 is RMA for each "spot" or probe
Level 3 is RMA by gene (which should be same as probe-set), but I am unclear how they summarize each probe-set (average?). I think what I need to do is ask them for more details.


-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at med.umich.edu]
Sent: Monday, January 12, 2009 1:06 PM
To: Skewes,Aaron
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] Probe-level rma vs. gene-level rma in "Affy"

Hi Aaron,

Can you clarify this a bit? By probe-level rma do you mean
probeset-level? What do you mean by gene-level?



Skewes,Aaron wrote:
> Hello,
> Can anybody advise me on how to get gene-level rma vs. probe-level rma using  rma(...) method in the Affy package for the HTHGU133A platform?
> Thank You,
> Aaron
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James W. MacDonald, M.S.
Hildebrandt Lab
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