Question: tissue contamination problem in microarray
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gravatar for Hao Liu
15.3 years ago by
Hao Liu130
Hao Liu130 wrote:
Dear All: 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. Best regards Hao Liu, Ph. D
breast lung • 545 views
ADD COMMENTlink modified 15.3 years ago by Oosting, J. PATH550 • written 15.3 years ago by Hao Liu130
Answer: tissue contamination problem in microarray
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gravatar for Wolfgang Huber
15.3 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k 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
ADD COMMENTlink written 15.3 years ago by Wolfgang Huber13k
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
ADD REPLYlink written 15.3 years ago by Hao Liu130
Answer: tissue contamination problem in microarray
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gravatar for lgautier@altern.org
15.3 years ago by
lgautier@altern.org950 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 suppose that experimentalists did their best when performing the biopsy, and that you have to deal with the mix of tissues the best you can. I remember seeing a talk at ISMB addressing the issue: http://bioinformatics.oupjournals.org/cgi/content/abstract/17/suppl_1/ S279 (although I did not have the opportunity to dig the method or use it) Hopin' it helps, L.
ADD COMMENTlink written 15.3 years ago by lgautier@altern.org950
Answer: tissue contamination problem in microarray
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gravatar for Oosting, J. PATH
15.3 years ago by
Oosting, J. PATH550 wrote:
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@umdnj.edu] > Sent: dinsdag 4 mei 2004 06:25 > To: Wolfgang Huber > Cc: bioconductor@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 15.3 years ago by Oosting, J. PATH550
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