Difference between revisions of "Microarray diagnostics"
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=Summary statistics= | =Summary statistics= | ||
| − | Raw data should be on the 2<sup>16</sup> scale, with data ranges of (0, 65,535). Statistics of interest include, ''min'', ''max'',''range'', ''summary'',''# NA's'', ''# saturated'' for each slide, or for each block with slides. | + | Raw data should be on the 2<sup>16</sup> scale, with data ranges of (0, 65,535). Statistics of interest include, ''min'', ''max'',''range'', ''summary'',''# NA's'', ''# saturated'' for each slide, or for each block with slides. For each experiment, the number of ''Empty'', spots or ''positive/negative'' controls may be of interest from the annotation information. |
==Examples using apply== | ==Examples using apply== | ||
Revision as of 01:41, 6 September 2006
Summary statistics
Raw data should be on the 216 scale, with data ranges of (0, 65,535). Statistics of interest include, min, max,range, summary,# NA's, # saturated for each slide, or for each block with slides. For each experiment, the number of Empty, spots or positive/negative controls may be of interest from the annotation information.
Examples 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))
