[BioC] Note on xps and tRMA

[cstrato]

Dear Mark,

Yes, my implementation of tRMA applies to all arrays including oligo/ST 
arrays.

BTW, I forgot to mention that the authors of the paper include the 
R-package "trma" as supplementary file "supp12.gz" to their paper, I am 
sorry for this omission.

Best regards
Christian


On 12/3/10 2:02 AM, Mark Cowley 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
> -----------------------------------------------------
>