Description Usage Arguments Details Value References See Also Examples
Calculate bias metrics from an AffyBatch object. These are the original four bias metrics as described in the Genome Biology article.
1 | getBiasMetrics(x.batch, x.rma = rma(x.batch))
|
x.batch |
An |
x.rma |
An |
This function calculates four bias metrics for each microarray in a data set.
Three of the bias metrics are derived from the raw intensities in x.batch
and one is derived from the probeset-summarized expression values in x.rma
. If x.rma
is missing, the expression values will be computed using rma
.
A data frame containing bias metrics for each array.
pm.median |
Median intensity of all perfect-match probes on the array. |
pm.IQR |
Interquartile range of all perfect-match probes on the array. |
rma.IQR |
Interquartile range of all expression values on the array. |
degradation |
The slope returned by |
Eklund, A.C. and Szallasi, Z. (2008) Correction of technical bias in clinical microarray data improves concordance with known biological information. Genome Biology, 9:R26.
biasCorrection
; also qc
in the simpleaffy package.
1 2 3 4 | library(affydata)
data(Dilution)
bm <- getBiasMetrics(Dilution)
pairs(bm)
|
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