

-------- Original Message --------
Subject: 	Re: [R] ANOVA and Pseudoreplication in R
Date: 	Fri, 25 Feb 2011 12:10:14 -0800
From: 	Bert Gunter <gunter.berton@gene.com>
To: 	Ben Ward <benjamin.ward@bathspa.org>
CC: 	r-help <r-help@r-project.org>



I can hopefully save bandwidth here by suggesting that this belongs on
the R-sig-mixed-models list.

-- Bert

As an aside, shouldn't you be figuring this out yourself or seeking
local consulting expertise?

On Fri, Feb 25, 2011 at 9:08 AM, Ben Ward<benjamin.ward@bathspa.org>  wrote:
>  Hi, As part of my dissertation, I'm going to be doing an Anova, comparing
>  the "dead zone" diameters on plates of microbial growth with little paper
>  disks "loaded" with antimicrobial, a clear zone appears where death occurs,
>  the size depending on the strength and succeptibility. So it's basically 4
>  different treatments, and I'm comparing the diameters (in mm) of circles.
>  I'm concerned however, about Pseudoreplication and how to deal with it in R,
>  (I thought of using the Error() term.
>
>  I have four levels of one factor(called "Treatment"): NE.Dettol, EV.Dettol,
>  NE.Garlic, EV.Garlic.   ("NE.Dettol" is E.coli not evolved to dettol,
>  exposed to dettol to get "dead zones". And the same for NE.Garlic, but with
>  garlic, not dettol. "EV.Dettol" is E.coli that has been evolved against
>  dettol, and then tested afterwards against dettol to get the "dead zones".
>  Same applies for "EV.Garlic" but with garlic).  You see from the four levels
>  (or treatments) there are two chemicals involved. So my first concern is
>  whether they should be analysed using two seperate ANOVA's.
>
>  NE.Dettol and NE.Garlic are both the same organism - a lab stock E.coli,
>  just exposed to two different chemicals.
>  EV.Dettol and EV.Garlic, are in principle, likely to be two different forms
>  of the organism after the many experimental doses of their respective
>  chemical.
>
>  For NE.Garlic and NE.Dettol I have 5, what I've called "Lineages", basically
>  seperate bottles of them (10 in total).
>  Then I have 5 Bottles (Lineages) of EV.Dettol, and 5 of EV.Garlic. - This
>  was done because there was the possiblity that, whilst I'm expecting them
>  all to respond in a similar manner, there are many evolutionary paths to the
>  same result, and previous research and reading shows that occasionally one
>  or two react differently to the rest through random chance.
>  The point I observed above ("NE.Dettol and NE.Garlic are both the same
>  organism...") is also applicable to the 5 bottles: The 5 bottles each of
>  NE.Garlic and NE.Dettol are supposed to be all the same organism - from a
>  stock one kept in store in the lab.
>  There is potential though for the 5 of EV.Garlic, to be different from one
>  another, and potential for the 5 EV.Dettol to be different from one another.
>
>  The Lineage (bottle) is also a factor then, with 5 levels (1,2,3,4,5).
>  Because they may be different.
>
>  To get the measurements of the diamter of the zones. I take out a small
>  amount from a tube and spread it on a plate, then take three paper disks,
>  soaked in their respective chemical, either Dettol or Garlic. and press them
>  and and incubate them.
>  Then when the zones have appeared after a day or 2. I take 4 diameter
>  measurements from each zone, across the zone at different angles, to take
>  account for the fact, that there may be a weird shape, or not quite
>  circular.
>
>  I'm concerned about pseudoreplication, such as the multiple readings from
>  one disk, and the 5 lineages - which might be different from one another in
>  each of the Two "EV." treatments, but not with "NE." treatments.
>
>  I read that I can remove pseudoreplication from  the multiple readings from
>  each disk, by using the 4 readings on each disk, to produce a mean for the
>  disks, and analyse those means - Exerciseing caution where there are extreme
>  values. I think the 3 disks for each lineage themselves are not
>  pseudoreplication, because they are genuinley 3 disks on a plate: the "Disk
>  Diffusion Test" replicated 3 times - but the multiple readings from one disk
>  if eel, is pseudoreplication. I've also read about including Error() terms
>  in a formula.
>
>  I'm unsure of the two NE. Treatments comming from the same culture does not
>  introduce pseudoreplications at Treatment Factor Level, because of the two
>  different antimicrobials used have two different effects.
>
>  I was hoping for a more expert opinion on whether I have identified
>  pseudoreplication correctly or if there is indeed pseudoreplication in the 5
>  Lineages or anywhere else I haven't seen. And how best this is dealt with in
>  R. At the minute my solution to the multiple readings from one disk is to
>  simply make a new factor, with the means on and do Anova from that, or even
>  take the means before I even load the dataset into R. I'm wondering if an
>  Error() term would be correct.
>
>  Thanks,
>  Ben W.
>
>  ______________________________________________
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>  https://stat.ethz.ch/mailman/listinfo/r-help
>  PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>  and provide commented, minimal, self-contained, reproducible code.
>



-- 
Bert Gunter
Genentech Nonclinical Biostatistics




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