Difference between revisions of "Microarray diagnostics"
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Raw data should be on the 2<sup>16</sup> scale, with data ranges of (0, 65,535). | Raw data should be on the 2<sup>16</sup> scale, with data ranges of (0, 65,535). | ||
| − | Examples using apply over arrays in an ''RGList'' | + | Examples using apply over arrays in an ''RGList''. |
| + | =Using apply= | ||
<pre> | <pre> | ||
| − | # Maximums | + | # Maximums |
| − | apply(RG$R, 2, max, na.rm=TRUE) | + | apply(RG$R, 2, max, na.rm=TRUE) |
| − | apply(RG$Rb, 2, max, na.rm=TRUE) | + | apply(RG$Rb, 2, max, na.rm=TRUE) |
| − | apply(RG$G, 2, max, na.rm=TRUE) | + | apply(RG$G, 2, max, na.rm=TRUE) |
| − | apply(RG$Gb, 2, max, na.rm=TRUE) | + | apply(RG$Gb, 2, max, na.rm=TRUE) |
| − | # Examining backgrounds that are higher than foreground | + | # Examining backgrounds that are higher than foreground |
| − | apply(RG$R < RG$Rb, 2, sum, na.rm=TRUE) | + | apply(RG$R < RG$Rb, 2, sum, na.rm=TRUE) |
| − | apply(RG$G < RG$Gb, 2, sum, na.rm=TRUE) | + | apply(RG$G < RG$Gb, 2, sum, na.rm=TRUE) |
</pre> | </pre> | ||
Revision as of 01:17, 6 September 2006
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
# 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)
