I am looking for references to published papers on microarrays which
mention duplicate spots, i.e., replicate spots on the same array
containing
the same probe. The treatment of the duplicate spots can be very
brief,
e.g., just to say that log-ratios from duplicate spots were averaged
before
further analysis. I am particularly after papers in mainline
biological
journals. Any references would be much appreciated.
Thanks a lot
Gordon
Dear Gordon,
there is this paper in Cancer Cell from rather unknown scientists ;)
we
had 9200 spots all printed in dublicate:
Loss of a FYN-regulated differentiation and growth arrest pathway in
advanced stage neuroblastoma.
Bernd Berwanger, Oliver Hartmann, Eckhard Bergmann, Sandra Bernard,
Dirk
Nielsen, Michael Krause, Ali Kartal, Daniel Flynn, Ruprecht
Wiedemeyer,
Manfred Schwab, Helmut Sch?fer, Holger Christiansen, and Martin Eilers
Cancer Cell, 2002, Nov;2(5):377-86.
Cheers
-oli-
Date: Tue, 10 Feb 2004 09:02:44 +1100
From: Gordon Smyth <smyth@wehi.edu.au>
Subject: [BioC] Papers mentioning duplicate spots
To: BioC Mailing List <bioconductor@stat.math.ethz.ch>
Message-ID: <6.0.1.1.1.20040210085839.02907888@imaphost.wehi.edu.au>
Content-Type: text/plain; charset="us-ascii"; format=flowed
I am looking for references to published papers on microarrays which
mention duplicate spots, i.e., replicate spots on the same array
containing
the same probe. The treatment of the duplicate spots can be very
brief,
e.g., just to say that log-ratios from duplicate spots were averaged
before
further analysis. I am particularly after papers in mainline
biological
journals. Any references would be much appreciated.
Thanks a lot
Gordon
--
Oliver Hartmann
Epigenomics AG www.epigenomics.com Kastanienallee
24
+493024345329 10435
Berlin
Hi Gordon,
see also the paper below. We had duplicate spots per array, and
constructed a test statistic that adjusted for the correlations
between
them.
Best wishes
Wolfgang
Genome Res. 2001 Nov;11(11):1861-70.
Identification and classification of differentially expressed genes in
renal cell carcinoma by expression profiling on a global human
31,500-element cDNA array.
Boer JM, Huber WK, Sultmann H, Wilmer F, von Heydebreck A, Haas S,
Korn
B, Gunawan B, Vente A, Fuzesi L, Vingron M, Poustka A.
Department of Molecular Genome Analysis, German Cancer Research
Center,
Heidelberg, Germany.
PMID: 11691851 [PubMed - indexed for MEDLINE]
http://www.genome.org/cgi/content/full/11/11/1861
> Date: Tue, 10 Feb 2004 09:02:44 +1100
> From: Gordon Smyth <smyth@wehi.edu.au>
> Subject: [BioC] Papers mentioning duplicate spots
> To: BioC Mailing List <bioconductor@stat.math.ethz.ch>
> Message-ID: <6.0.1.1.1.20040210085839.02907888@imaphost.wehi.edu.au>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
>
> I am looking for references to published papers on microarrays which
> mention duplicate spots, i.e., replicate spots on the same array
containing
> the same probe. The treatment of the duplicate spots can be very
brief,
> e.g., just to say that log-ratios from duplicate spots were averaged
before
> further analysis. I am particularly after papers in mainline
biological
> journals. Any references would be much appreciated.
>
> Thanks a lot
> Gordon
>
-------------------------------------
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
Hi,
forgot to mention that unfortunately there was a typesetting error in
the printed version of the paper: On p.8, where it reads
S_phr = (a*T_phr- N_phr),
it should read
S_phr = sign(a*T_phr- N_phr),
Cheers,
Wolfgang
Wolfgang Huber wrote:
>
> see also the paper below. We had duplicate spots per array, and
> constructed a test statistic that adjusted for the correlations
between
> them.
>
> Genome Res. 2001 Nov;11(11):1861-70.
> Identification and classification of differentially expressed genes
in
> renal cell carcinoma by expression profiling on a global human
> 31,500-element cDNA array.
> Boer JM, Huber WK, Sultmann H, Wilmer F, von Heydebreck A, Haas S,
Korn
> B, Gunawan B, Vente A, Fuzesi L, Vingron M, Poustka A.
> Department of Molecular Genome Analysis, German Cancer Research
Center,
> Heidelberg, Germany.
>
> PMID: 11691851 [PubMed - indexed for MEDLINE]
> http://www.genome.org/cgi/content/full/11/11/1861
-------------------------------------
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
Well, this is so mainline you probably already have the ref.
Still, here it is:
http://www.pnas.org/cgi/content/abstract/101/5/1135
>
> Message: 6
> Date: Tue, 10 Feb 2004 09:02:44 +1100
> From: Gordon Smyth <smyth@wehi.edu.au>
> Subject: [BioC] Papers mentioning duplicate spots
> To: BioC Mailing List <bioconductor@stat.math.ethz.ch>
> Message-ID: <6.0.1.1.1.20040210085839.02907888@imaphost.wehi.edu.au>
> Content-Type: text/plain; charset="us-ascii"; format=flowed
>
> I am looking for references to published papers on microarrays which
> mention duplicate spots, i.e., replicate spots on the same array
> containing
> the same probe. The treatment of the duplicate spots can be very
> brief,
> e.g., just to say that log-ratios from duplicate spots were averaged
> before
> further analysis. I am particularly after papers in mainline
> biological
> journals. Any references would be much appreciated.
>
> Thanks a lot
> Gordon
>
