[BioC] Note on xps and tRMA

[Henrik Bengtsson]

For what it's worth,

there are different ways to estimate the log-additive probe level
model of RMA.  The median polish estimator is known to have some
flaws, e.g. it can oscillate between two estimates.  The robust linear
model M-estimator has nice properties, also gives estimates of
standard errors.  Since several years, Ben Bolstad provides a very
solid and fast implementation in the preprocessCore package, which
also handles probe-by-probe missing values and probe-by-probe weights.
 See for instance

  help("rcModelPLM", package="preprocessCore")

I highly recommend to use that for estimating this PLM model instead
of median polish.

/Henrik

On Thu, Dec 2, 2010 at 5:02 PM, Mark Cowley <m.cowley at garvan.org.au> wrote:
> Hi Christian,
> That's VERY interesting.
> I've observed identical expression levels across probesets in newer ST
> arrays, (& now that the authors mention it, probably more frequently
> with odd numbers of arrays), but I can't say i've ever noticed the
> phenomena in the older 3' arrays.
>
> Does your implementation of tRMA also apply to oligo/ST arrays?
>
> cheers,
> Mark
>
> On 03/12/2010, at 8:17 AM, cstrato wrote:
>
>> Dear All,
>>
>> Recently I found an interesting paper about problems with RMA when
>> applied to small sample sets which are based on the median-polish
>> algorithm, see:
>> http://www.biomedcentral.com/1471-2105/11/553/abstract
>>
>> Since the authors offer a simple solution to the problem I thought
>> it might be of interest to users that I have implemented function
>> "trma()" in the development version "xps_1.11.3".
>>
>> Best regards
>> Christian
>> _._._._._._._._._._._._._._._._._._
>> C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
>> V.i.e.n.n.a           A.u.s.t.r.i.a
>> e.m.a.i.l:        cstrato at aon.at
>> _._._._._._._._._._._._._._._._._._
>>
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>
>
> -----------------------------------------------------
> Mark Cowley, PhD
>
> Peter Wills Bioinformatics Centre
> Garvan Institute of Medical Research, Sydney, Australia
> -----------------------------------------------------
>
>
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