[R-sig-ME] Fwd: Re: [R] ANOVA and Pseudoreplication in R

Ben Ward benjamin.ward at bathspa.org
Sat Feb 26 16:44:56 CET 2011

On 25/02/2011 21:22, Ben Ward wrote:
> -------- Original Message --------
> Subject: 	Re: [R] ANOVA and Pseudoreplication in R
> Date: 	Fri, 25 Feb 2011 12:10:14 -0800
> From: 	Bert Gunter<gunter.berton at gene.com>
> To: 	Ben Ward<benjamin.ward at bathspa.org>
> CC: 	r-help<r-help at 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?

I did consult with the lecturer at university that knows most about 
stats, and he advised me:

"Pseudo replication is really about a lack of independence between measurements, So you need to work backwards and see where you are building in a known lack of independence.  And where that is the case you need to use means of all the values."

And I have done this and came to the conclusion I mentioned as to where 
I thought Pseudoreplicaton was comming from, however, I do not know 
about the one other 'potential' source as it really is for me at least, 
a grey area.
I've consulted a few forums that deal with the theory more and await any 
response. Until then I'll have to try and get as many opinions on it as 

-Ben W.

> On Fri, Feb 25, 2011 at 9:08 AM, Ben Ward<benjamin.ward at 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.
>>   ______________________________________________
>>   R-help at r-project.org mailing list
>>   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.

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