Hi all,
I'm having some trouble in understanding how to ste the Error() term in
the aov() function when fitting a hierarchical ANOVA.
I have data concerning the expression of 2 miRNAs in 3 different cell
lines, with 2 different extraction methods. The data is organized as
follows :
Line Extraction Target Expression
1 BC54 miRNA RNU48 22.48
2 BC54 miRNA RNU48 22.36
3 BC54 miRNA 221 26.49
4 BC54 miRNA 221 26.42
5 BC54 RNAtot RNU48 22.95
6 BC54 RNAtot RNU48 22.98
7 BC54 RNAtot 221 26.35
8 BC54 RNAtot 221 26.43
9 BC108 miRNA RNU48 24.19
10 BC108 miRNA RNU48 24.01
11 BC108 miRNA 221 29.94
12 BC108 miRNA 221 29.61
13 BC108 RNAtot RNU48 22.42
14 BC108 RNAtot RNU48 22.29
15 BC108 RNAtot 221 26.79
16 BC108 RNAtot 221 26.73
17 BC233 miRNA RNU48 21.84
18 BC233 miRNA RNU48 21.69
19 BC233 miRNA 221 25.95
20 BC233 miRNA 221 25.98
21 BC233 RNAtot RNU48 22.55
22 BC233 RNAtot RNU48 22.58
23 BC233 RNAtot 221 25.11
24 BC233 RNAtot 221 25.45
For the two miRNA and for each cell line I want to compare the
expression value between the two extraction methods. As there are no
random effects I tried to use the aov() function to do so. I don't know
which of the two following models is the "good" one :
This one :
> mir221.aov=aov(Ct~Extraction+Error(Target/Line/Extraction),data=mir221)
with this model the extraction has no significant effect :
> summary(mir221.aov)
Error: Target
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 1 99.675 99.675
Error: Target:Line
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 4 16.9779 4.2445
Error: Target:Line:Extraction
Df Sum Sq Mean Sq F value Pr(>F)
Extraction 1 2.8912 2.8912 1.3568 0.2966
Residuals 5 10.6545 2.1309
Error: Within
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 12 0.164150 0.013679
or this one :
> mir221.aov=aov(Ct~Extraction+Error(Target/Line),data=mir221)
with this model the extraction has a significant effect:
> summary(mir221.lm)
Error: Target
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 1 99.675 99.675
Error: Target:Line
Df Sum Sq Mean Sq F value Pr(>F)
Residuals 4 16.9779 4.2445
Error: Within
Df Sum Sq Mean Sq F value Pr(>F)
Extraction 1 2.8912 2.8912 4.5431 0.04794 *
Residuals 17 10.8187 0.6364
Could you please help me understanding which is the right model for my
question ? Thanks by advance
Jonas Mandel
U900 - Bioinformatics unit
Institut Curie
Paris
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