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

Matthew McCall mccallm at gmail.com
Mon Mar 5 23:21:31 CET 2012


The probe-effects (probeVec) are not a baseline expression -- they are
constrained to sum to zero within each probeset, so they represent the
typical difference from the overall probeset expression.


On Mon, Mar 5, 2012 at 5:14 PM, Robert Castelo <robert.castelo at upf.edu> wrote:
> 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 paper.
> 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.
> cheers,
> robert.
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Matthew N McCall, PhD
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