[BioC] how to rank affy probesets by their probe-effect magnitude

Robert Castelo robert.castelo at upf.edu
Mon Mar 5 23:14:09 CET 2012

hi Jim,

On 3/5/12 8:02 PM, James W. MacDonald wrote:

> I'm not sure what you are looking to do with these data, but remember
> that the probe-specific effects in RMA are estimated as a nuisance
> variable, which are then excluded from computation of the expression
> value. So by definition the probesets should not be affected by
> probe-specific effects.

my understanding is that probesets in a microarray may have different 
baseline expression levels due to probe-specific effects. if i recall 
correctly this is illustrated in Fig. 1 of Zilliox and Irizarry (Nat. 
Meth., 2007) and this, for instance, complicates the question of 
determining whether a gene is expressed or not, which is tackled on that 

i would like to assess somehow the agreement of these possibly different 
expression baselines between different genes and i thought that 
probe-specific effects would contain such information.

to be more specific, if we would assume a simple additive model

y_ij = probe_effect_i + sample_effect_j + noise_ij

i'd like to know what genes have more similar or more disparate probe 
effects estimated as the probe_effect_i term in the previous linear 
model and i thought such information could be extracted from PLMset objects.


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