[BioC] RE:proper pooling design

[Kenny Ye]

what is the purpose of your experiment? if it is simply comparing several
groups, speaking in the language of experimental design, you should treat
each sample collection period (i.e. days) as blocks and use randomized
block design. the blocking factor will also be included in your data
analysis (one more factor in your anova, make it two way ANOVA). here is
an introduction on the website of
http://www.itl.nist.gov/div898/handbook/pri/section3/pri332.htm

If your experiment is more complicated than one treatment factors, you
need more complicated designs. please send me personal emails.

Kenny


Kenny Ye
Assistant Professor
Department of Applied Math and Statistics
SUNY at  Stony Brook
Stony Brook, New York 11794-3600
Phone (631)632-9344
Fax   (631)632-8490

On Fri, 23 Jan 2004, YUK FAI LEUNG wrote:

> Hi,
> 
> There is another issue that comes up from my discussion with some people 
> about my earlier question on pooling design. It is very likely that I 
> can't collect all the samples in one day, not even the pooled biological 
> replicates. I have heard many people say that the time of collection 
> (i.e. day) has a great effect on resulting clustering etc. data 
> analysis. I guess this might be true in some cases,  although I haven't 
> looked into this factor seriously. I would if anyone has any experiences 
> on this.
> 
> If this effect is true in my case, then the variation among the 
> biological replicates might be larger than it should be, which I want to 
> avoid. Could someone suggest a sequence of sample collection based on a 
> proper statisical design which can avoid/minimize such collection-time 
> variation on data analysis?
> 
> Thanks!
> 
> Best regards,
> Fai
> -- 
> Yuk Fai Leung
> Department of Molecular and Cellular Biology
> Harvard University
> BL 2079, 16 Divinity Avenue
> Cambridge, MA 02138
> Tel: 617-495-2599
> Fax: 617-496-3321
> email: yfleung at mcb.harvard.edu; yfleung at genomicshome.com
> URL: http://genomicshome.com
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
>