I would like to check for differences in growth rate between groups. I have three main groups miRs
and for each group I have a treatment
and a Neg
. I want to compare treatment vs Neg for all groups.
Could someone have a look at my setup?
Why is the variable mir-135b-5p
nor showing up in the results?
> lm <- lme(weight~time*cond, random=~time|miRs, data=testDose)
> anova(lm)
numDF denDF F-value p-value
(Intercept) 1 38 233748.85 <.0001
time 1 38 398.12 <.0001
cond 3 38 7.14 0.0006
time:cond 3 38 2.34 0.0887
> summary(lm)
Linear mixed-effects model fit by REML
Data: testDose
AIC BIC logLik
51.94759 72.21414 -13.97379
Random effects:
Formula: ~time | miRs
Structure: General positive-definite, Log-Cholesky parametrization
StdDev Corr
(Intercept) 3.279719e-06 (Intr)
time 9.458478e-10 0
Residual 1.951541e-01
Fixed effects: weight ~ time * cond
Value Std.Error DF t-value p-value
(Intercept) 12.322245 0.16900842 38 72.90906 0.0000
time 0.021713 0.00257138 38 8.44398 0.0000
condmir-21-3p 0.048565 0.23901400 38 0.20319 0.8401
condmir-584-5p 0.125029 0.23901400 38 0.52310 0.6039
condNeg 0.021297 0.19515412 38 0.10913 0.9137
time:condmir-21-3p -0.002460 0.00363648 38 -0.67658 0.5028
time:condmir-584-5p -0.006198 0.00363648 38 -1.70431 0.0965
time:condNeg 0.001352 0.00296918 38 0.45549 0.6513
Correlation:
(Intr) time c-21-3 c-584- condNg t:-21- t:-584
time -0.913
condmir-21-3p -0.707 0.645
condmir-584-5p -0.707 0.645 0.500
condNeg -0.866 0.791 0.612 0.612
time:condmir-21-3p 0.645 -0.707 -0.913 -0.456 -0.559
time:condmir-584-5p 0.645 -0.707 -0.456 -0.913 -0.559 0.500
time:condNeg 0.791 -0.866 -0.559 -0.559 -0.913 0.612 0.612
Standardized Within-Group Residuals:
Min Q1 Med Q3 Max
-1.4935997 -0.5794501 -0.2101814 0.4779404 1.4872837
Number of Observations: 48
Number of Groups: 3
myData
> testDose
weight time cond miRs
1 13.10760 24 mir-21-3p mir-21-3p
2 13.21659 48 mir-21-3p mir-21-3p
3 13.59320 72 mir-21-3p mir-21-3p
4 14.18753 96 mir-21-3p mir-21-3p
5 13.16919 24 Neg mir-21-3p
6 13.51846 48 Neg mir-21-3p
7 14.05866 72 Neg mir-21-3p
8 14.84804 96 Neg mir-21-3p
9 12.79820 24 mir-21-3p mir-21-3p
10 13.12730 48 mir-21-3p mir-21-3p
11 13.69247 72 mir-21-3p mir-21-3p
12 14.48472 96 mir-21-3p mir-21-3p
13 12.81832 24 Neg mir-21-3p
14 13.17344 48 Neg mir-21-3p
15 13.78877 72 Neg mir-21-3p
16 14.44471 96 Neg mir-21-3p
17 13.11672 24 mir-135b-5p mir-135b-5p
18 13.31708 48 mir-135b-5p mir-135b-5p
19 13.78559 72 mir-135b-5p mir-135b-5p
20 14.54087 96 mir-135b-5p mir-135b-5p
21 13.16919 24 Neg mir-135b-5p
22 13.51846 48 Neg mir-135b-5p
23 14.05866 72 Neg mir-135b-5p
24 14.84804 96 Neg mir-135b-5p
25 12.79218 24 mir-135b-5p mir-135b-5p
26 13.18126 48 mir-135b-5p mir-135b-5p
27 13.78006 72 mir-135b-5p mir-135b-5p
28 14.48629 96 mir-135b-5p mir-135b-5p
29 12.81832 24 Neg mir-135b-5p
30 13.17344 48 Neg mir-135b-5p
31 13.78877 72 Neg mir-135b-5p
32 14.44471 96 Neg mir-135b-5p
33 13.06603 24 mir-584-5p mir-584-5p
34 13.10624 48 mir-584-5p mir-584-5p
35 13.27287 72 mir-584-5p mir-584-5p
36 13.96981 96 mir-584-5p mir-584-5p
37 13.16919 24 Neg mir-584-5p
38 13.51846 48 Neg mir-584-5p
39 14.05866 72 Neg mir-584-5p
40 14.84804 96 Neg mir-584-5p
41 12.81925 24 mir-584-5p mir-584-5p
42 13.03732 48 mir-584-5p mir-584-5p
43 13.59867 72 mir-584-5p mir-584-5p
44 14.15521 96 mir-584-5p mir-584-5p
45 12.81832 24 Neg mir-584-5p
46 13.17344 48 Neg mir-584-5p
47 13.78877 72 Neg mir-584-5p
48 14.44471 96 Neg mir-584-5p