[BioC] (no subject)

Furge, Kyle Kyle.Furge at vai.org
Tue Jul 12 16:58:33 CEST 2005

There was a thread about single condition analysis a while back. Search the
BioC archives for "GCRMA: low intensity exprs estimates" for a brief
discussion on possible methods to estimate if a transcript is expressed or

However, as mentioned earlier this type of analysis not routinely performed
and is mostly in the exploratory phases. As such, it is not clear if a
standard set of a->b->c method/thresholds could quickly be applied.


> From: "Marta Agudo" <martabar at um.es>
> Date: Tue, 12 Jul 2005 11:38:09 +0200
> To: <Bioconductor at stat.math.ethz.ch>
> Subject: [BioC] (no subject)
> Hi there
> I´ve been thinking about gene expression in just one condition without
> comparing to anything else.
> I explain better: I have data from an  affy array experiment using naive
> tissue RNA, and I want to know which genes, out of the 30000 present in the
> chip, are being expressed in this tissue.
> I would like to know  is this analysis is  possible, i mean not just
> statistically but also if scientifically has any sense,
> And if it is I would need some help
> a) is it possible to use bioconductor and GCRMA analysis ? then,  anyone
> knows a script or could guide me?
> b) how many replicas  do we need?
> c) which is the cut off point?
> Basically which are the pros and the cons of this kind of analysis?
> thank you very much!
> marta
> Marta Agudo PhD
> Departamento de Oftalmología
> Facultad de Medicina
> Campus Espinardo
> 30100 Murcia- Spain
> Phone:+34 968363996
> [[alternative HTML version deleted]]
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