[R-sig-ME] Mixed Models - remedy for pseudoreplication?

[Jens Oldeland]

Dear Thierry,


> lme(response  ~ treatment, random =  ~1|day)

In fact, this is exactly what we did. The problem we have that there 469 
degrees of freedom. By averaging there are only 6 dfs left.
Thus the question was "are we inflating our df's" due to 
pseudoreplication or are the single wells 'good' replications.

Due to the high intra-day variability, I was thinking a LME would be 
justified. but maybe I am wrong.

thank you Thierry
Jens


Am 30.07.2013 17:11, schrieb ONKELINX, Thierry:
> Dear Jens,
>
> I would suggest that you make a list of all elements in you design that can influence the result: e.g. treatment, tube, flask, day, plate, column, day:flask interaction, ...
> - Eliminate the non-relevant ones (e.g. maybe column).
> - Eliminate the ones that have only one level (flask?)
> - Some will be confounding. If you have only one flask and do one plate each day, then you cannot separate the effect of day, plate and the interaction of day and flask. You have to choose one (e.g. day) and this will model the combined effect. If you want to separate those effects, then you will have to change your design.
> - Make a model with the remain variables. lme(response  ~ treatment, random =  ~1|day) might be what you need.
>
> Best regards,
>
> ir. Thierry Onkelinx
> Instituut voor natuur- en bosonderzoek / Research Institute for Nature and Forest
> team Biometrie & Kwaliteitszorg / team Biometrics & Quality Assurance
> Kliniekstraat 25
> 1070 Anderlecht
> Belgium
> + 32 2 525 02 51
> + 32 54 43 61 85
> Thierry.Onkelinx at inbo.be
> www.inbo.be
>
> To call in the statistician after the experiment is done may be no more than asking him to perform a post-mortem examination: he may be able to say what the experiment died of.
> ~ Sir Ronald Aylmer Fisher
>
> The plural of anecdote is not data.
> ~ Roger Brinner
>
> The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
>
>
> -----Oorspronkelijk bericht-----
> Van: Jens Oldeland [mailto:fbda005 at uni-hamburg.de]
> Verzonden: dinsdag 30 juli 2013 16:14
> Aan: ONKELINX, Thierry
> CC: r-sig-mixed-models at r-project.org
> Onderwerp: Re: [R-sig-ME] Mixed Models - remedy for pseudoreplication?
>
> Dear Thierry,
>
> sorry for beeing imprecise, I provided clearer details below
>
>
> - do you create 6 plates on day 0 and measure them on day 1, 2, ... or do you fill a new plate each day with the content of the flasks?
>> We filled a new plate each day and the contents of the flasks also were newly mixed every day. However, the source within the flasks remained the same, i.e. cancer cells.
> - how are the flasks distributed over the plates? Each well come for a different flask? Or all wells from the same column come from one flash?
>> every day the content of one newly mixed solution was put on a 96 well plate. on the plate, different treatments were applied. thus, the content from the flask was always the same however differed per day due to slightly different temperatures in the lab per day etc. so all columns receive the same material from the flask, but different treatments were applied (per column) that should reduce growth of cancer cells.
>
> So to say, there was one set of materials (flasks, cancer cells, tubes) that were mixed together on 6 different days, every day a new set uo was produced.
>
> thank you already!
>
>
> --
> +++++++++++++++++++++++++++++++++++++++++
> Dr. Jens Oldeland
>
> Post-Doc Researcher & Lecturer @ BEE
> Managing Editor - Biodiversity & Ecology
>
> Biodiversity, Ecology and Evolution of Plants (BEE) Biocentre Klein Flottbek and Botanical Garden University of Hamburg Ohnhorststr. 18
> 22609 Hamburg,
> Germany
>
> Tel:    0049-(0)40-42816-407
> Fax:    0049-(0)40-42816-543
> Mail:   jens.oldeland at uni-hamburg.de
>           Oldeland at gmx.de
> Skype:  jens.oldeland
> http://www.biologie.uni-hamburg.de/bzf/fbda005/fbda005.htm
> http://www.biodiversity-plants.de/biodivers_ecol/biodivers_ecol.php
> +++++++++++++++++++++++++++++++++++++++++
>
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-- 
+++++++++++++++++++++++++++++++++++++++++
Dr. Jens Oldeland

Post-Doc Researcher & Lecturer @ BEE
Managing Editor - Biodiversity & Ecology

Biodiversity, Ecology and Evolution of Plants (BEE)
Biocentre Klein Flottbek and Botanical Garden
University of Hamburg
Ohnhorststr. 18
22609 Hamburg,
Germany

Tel:    0049-(0)40-42816-407
Fax:    0049-(0)40-42816-543
Mail: 	jens.oldeland at uni-hamburg.de
         Oldeland at gmx.de 	
Skype:	jens.oldeland
http://www.biologie.uni-hamburg.de/bzf/fbda005/fbda005.htm
http://www.biodiversity-plants.de/biodivers_ecol/biodivers_ecol.php
+++++++++++++++++++++++++++++++++++++++++