[BioC] tissue contamination problem in microarray

[Oosting, J. (PATH)]

Hi Hao,

In our lab we resort to the viewpoint that any contaminated stromal or
myeloid tissue is usually close enough to the tissue of interest that it is
in interaction with it. You would probably also find changes in gene
expression in these celltypes compared to unaffected stromal tissue.
Only in situ methods will tell you in which tissue type the change has taken
place.

Jan

> -----Original Message-----
> From: Hao Liu [mailto:liuha at umdnj.edu]
> Sent: dinsdag 4 mei 2004 06:25
> To: Wolfgang Huber
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] tissue contamination problem in microarray
> 
> 
> hi! Wolfgang:
> 
> I actually talked with some very good pathologists, according to them
> even microdissected sample (cancer tissue) could have around 20%
> contamination from surrounding tissue.
> 
> Your answer to  my question makes me wonder if I heard is true, can
> someone help to clarify this issue? Thanks
> 
> Best
> Hao
> 
> On Mon, 3 May 2004, Wolfgang Huber wrote:
> 
> > 
> > 
> > Hao Liu wrote:
> > > 
> > > I would like to know if there are techniques to minimize 
> the perturbation
> > > caused by tissue contamination, for example, normal lung tissue
> > > contamination on a breast metastasis. What is the best 
> strategy to deal
> > > with this problem? 
> > > 
> > > I think this should be dealt with at the "low" level normalization
> > > process, please help.
> > 
> > I think it should be dealt with at the level of tissue 
> extraction, i.e. 
> > use microdissection.
> > 
> > Best wishes
> >    Wolfgang
> > 
> > -- 
> > -------------------------------------
> > Wolfgang Huber
> > Division of Molecular Genome Analysis
> > German Cancer Research Center
> > Heidelberg, Germany
> > Phone: +49 6221 424709
> > Fax:   +49 6221 42524709
> > Http:  www.dkfz.de/abt0840/whuber
> > -------------------------------------
> > 
> 
> Best regards
> 
> Hao Liu, Ph. D
> 
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