Gene expression levels from two-color dye-swap experiment on 6 microarrays. Arrays 1 and 2 represent the first biological sample (ie, the first dye swap), 3 and 4 the second, and arrays 5 and 6 the third.
A data frame with 258000 observations on the following 5 variables.
a factor with levels green red
representing the dye used for the gene expression
a
factor with levels 1 2 3 4 5 6
corresponding to the 6 arrays
a factor with 21500 levels representing the genes on the arrays
a factor
with levels rnt wt for the two types of plants: runts and wild
type
a numeric vector with the gene expression level (normalized but not log transformed)
Data provided by Soren Bak <bak@life.ku.dk>. Added by Claus Ekstrom <ekstrom@sund.ku.dk>
Morant, M. et al. (2010). Metabolomic, Transcriptional, Hormonal and Signaling Cross-Talk in Superroot2. Molecular Plant. 3, p.192--211.
data(superroot2) # Select one gene g1 <- superroot2[superroot2$gene=="AT2G24000.1",] model <- lm(log(signal) ~ plant + color + array, data=g1) summary(model)#> #> Call: #> lm(formula = log(signal) ~ plant + color + array, data = g1) #> #> Residuals: #> 1 2 3 4 5 6 129001 129002 #> 0.11605 0.11167 -0.13984 -0.07720 0.02379 -0.03447 -0.11605 -0.11167 #> 129003 129004 129005 129006 #> 0.13984 0.07720 -0.02379 0.03447 #> #> Coefficients: #> Estimate Std. Error t value Pr(>|t|) #> (Intercept) 6.39677 0.13318 48.032 1.12e-06 *** #> plantwt -0.04857 0.09417 -0.516 0.633236 #> colorred 0.17805 0.09417 1.891 0.131649 #> array2 -1.55889 0.16311 -9.557 0.000669 *** #> array3 -0.71928 0.16311 -4.410 0.011603 * #> array4 -0.38153 0.16311 -2.339 0.079453 . #> array5 -0.80767 0.16311 -4.952 0.007752 ** #> array6 -0.46209 0.16311 -2.833 0.047202 * #> --- #> Signif. codes: 0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 #> #> Residual standard error: 0.1631 on 4 degrees of freedom #> Multiple R-squared: 0.9643, Adjusted R-squared: 0.9018 #> F-statistic: 15.43 on 7 and 4 DF, p-value: 0.00946 #>