Microarray diagnostics

Summary statistics

Raw data should be on the 2¹⁶ scale, with data ranges of (0, 65,535).

Examples using apply over arrays in an RGList.

Using apply

 # Ranges
 apply(RG$R, 2, range, na.rm=TRUE)
 apply(RG$G, 2, range, na.rm=TRUE)
 # Maximums
 apply(RG$R, 2, max, na.rm=TRUE)
 apply(RG$Rb, 2, max, na.rm=TRUE)
 apply(RG$G, 2, max, na.rm=TRUE)
 apply(RG$Gb, 2, max, na.rm=TRUE)
 # Examining backgrounds that are higher than foreground
 apply(RG$R < RG$Rb, 2, sum, na.rm=TRUE)
 apply(RG$G < RG$Gb, 2, sum, na.rm=TRUE)

There are several times where the data ranges, or the number of introduced missing values (NA's) can be investigated during background correction and normalization.

Background Correction

# Number of missing values
 apply( backgroundCorrect(RG, method="subtract"), 2, sum(is.na))