[BioC] Experimental design for RNA-Seq

[michael watson (IAH-C)]

Great stuff, thanks Steve and Naomi.

I guess I was thinking of technical replicates simply as sequencing the same library on multiple occasions;  though creating two libraries out of one sample adds an extra layer of complexity.

What is the evidence (if any) that lane and/or library preparation can have an effect?

To adjust for lane effects, I guess one could multiplex each sample so that they're run on all lanes, and combine the counts at the end?

Hmmm
Mick

-----Original Message-----
From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] 
Sent: 28 May 2010 16:01
To: Naomi Altman
Cc: michael watson (IAH-C); bioconductor
Subject: Re: [BioC] Experimental design for RNA-Seq

Hi,

I just wanted to ask/make one point.

On Fri, May 28, 2010 at 9:17 AM, Naomi Altman <naomi at stat.psu.edu> wrote:
> At least from the stat theory point of view, the best design is equal
> numbers of biological samples (the more the better) for each condition and
> no technical reps.

Can you clarify a bit as to what you are referring to as a "technical
replicate" in this sense?

You could consider two lanes that are sequenced from the same library
as technical replicates, no? Or, by "technical replicate" do you mean
creating two libraries out of one sample?

If we're talking about the former, then I think there is lots of value
to be gained, and perhaps necessary(?), to running more than one lane
per library preparation -- and maybe the question would rather be "how
many lanes to run per library"?

What does the court think?

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact