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
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~ Sir Ronald Aylmer Fisher
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-----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!
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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
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