Dear Ingunn

There are a number of interesting papers on reproducibility of NGS results.

't Hoen, PA, Ariyurek, Y, Thygesen, HH, 
Vreugdenhil, E, Vossen, RH, de Menezes, RX, Boer, 
JM, van Ommen, GJ & den Dunnen, JT 2008, 'Deep 
sequencing-based expression analysis shows major 
advances in robustness, resolution and inter-lab 
portability over five microarray platforms', 
Nucleic Acids Research, vol. 36, no. 21, p. e141.

Marioni, JC, Mason, CE, Mane, SM, Stephens, M & 
Gilad, Y 2008, 'RNA-seq: an assessment of 
technical reproducibility and comparison with 
gene expression arrays', Genome Res, vol. 18, no. 9, pp. 1509-17.

Bullard, JH, Purdom, EA, Hansen, KD, Durinck, S & 
Dudoit, S 2009, 'Statistical Inference in 
mRNA-Seq: Exploratory Data Analysis and 
Differential Expression', U.C. Berkeley, 247.

Naomi


At 03:16 AM 2/1/2010, you wrote:
>Dear Dr. Altman
>
>I send this off the bioconductor mail list as it 
>is more of a NGS question than an R question.
>I am curious about how the reproducibility 
>between biological replicates usually is. I send 
>this question to you since you answered the more 
>technical question about how to measure it, you 
>may have some experience about it. I am not 
>currently involved in any projects on NGS, but 
>want to keep updated and this question is very 
>relevant for planning experiments. I hope for an informative reply.
>
>Best regards
>
>Ingunn Berget (Dr. Scient)
>UMB, box 5003, IHA
>1432 Ås
>Norway
>
>Centre for Integrative Genetics, www.cigene.no
>Centre for Biospectroscopy and Data Modelling, www.specmod.org
> >-----Original Message-----
> >From: bioconductor-bounces@stat.math.ethz.ch 
> [<mailto:bioconductor->mailto:bioconductor-
> >bounces@stat.math.ethz.ch] On Behalf Of Naomi Altman
> >Sent: Saturday, January 30, 2010 4:10 AM
> >To: Pete Shepard; bioconductor@stat.math.ethz.ch; bioc-sig-sequencing-
> >request@r-project.org
> >Subject: Re: [BioC] reproducibility between reads?
> >
> >cor(log(count.sample1+.25),log(count.sample2+.25)) works pretty well.
> >
> >--Naomi
> >
> >At 05:57 PM 1/29/2010, Pete Shepard wrote:
> >>Dear List,
> >>
> >>I am attempting to measure the reproducibility of two biological
> >replicate
> >>RNA seq Solexa reads. Are there any Bioconductor packages that can
> >handle
> >>this?
> >>
> >>TIA
> >>
> >>         [[alternative HTML version deleted]]
> >>
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> >
> >Naomi S. Altman                                814-865-3791 (voice)
> >Associate Professor
> >Dept. of Statistics                              814-863-7114 (fax)
> >Penn State University                         814-865-1348 (Statistics)
> >University Park, PA 16802-2111
> >
> >_______________________________________________
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111

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