Description Usage Arguments Details Value Author(s) References See Also Examples
Correction of plate and spatial effects of the data xraw
of a cellHTS
object using the B score method.
Using this method, a two-way median polish is fitted in a per-plate basis to account for row and column effects.
Optionally, the obtained residuals within each plate can be further divided by their median absolute deviations to standardize for plate-to-plate variability.
Optionally, a transformation to z-scores can be performed.
1 |
x |
a |
what |
a character indicating the slot of |
adjustPlateMedian |
a logical value indicating whether the estimated average of each plate should also be subtracted to the raw intensity values. |
scale |
a logical value indicating if the per-plate model residuals should be further scaled by their variance. See details. |
save.model |
a logical value specifying whether the per-plate models should be saved, and given as output. See details. |
The normalization is performed in a per-plate fashion using the B score method.
This function can be called direclty, or indirectly, using normalizePlates
or
summarizeChannels
.
In the B score method, the residual r_{ijp} of the measurement for row i and column j on the p-th plate is obtained by fitting a two-way median polish, in order to account for both row and column effects within the plate:
r_{ijp} = y_{ijp} - yest_{ijp} = y_{ijp} - (mu_p + R_{ip} + C_{jp})
y_{ijp} is the measurement value in row i and column j of plate p (taken from x$xraw
), and
yest_{ijp} is the corresponding fitted value.
This is defined as the sum between the estimated average
of the plate (mu_p), the estimated systematic offset for row i
(R_{ip}), and the systematic offset for column j (C_{jp}).
If scale=TRUE
, for each plate p, each of the obtained residual values r_{ijp}'s are divided by the median absolute deviation of the residuals in plate p (MAD_p), giving the B score value:
Bscore_{ijp} = r_{ijp}/MAD_p
If adjustPlateMedian
is set to FALSE
, the estimated overall plate average
(mu_p) is not removed from the intensity values y_{ijp}'s.
If save.model=TRUE
, the models residuals (r_{ijp}'s), row and column offsets and overall offsets are stored in the slots residuals
, rowcol.effects
and overall.effects
of the cellHTS
object x
.
An object of class cellHTS
, which is a copy of the argument
x
, plus an additional slot xnorm
containing the normalized
data. This is an array of the same dimensions as xraw
.
Furthermore, if save.model=TRUE
, the slots residuals
, rowcol.effects
, and overall.effects
(only if adjustPlateMedian
was also set to TRUE
) are added to x
.
The latter slots are arrays with the same dimension as x$xraw
, except the
overall.effects
,
which have dimensions 1 x nr Plates x nr Replicates x nr Channels
.
Moreover, the processing status of the cellHTS
object is updated
in the slot state
to x$state["normalized"]=TRUE
.
Ligia Braz ligia@ebi.ac.uk
Brideau, C., Gunter, B., Pikounis, B. and Liaw, A. (2003) Improved statistical methods for hit selection in high-throughput screening, J. Biomol. Screen 8, 634–647.
Malo, N., Hanley, J.A., Cerquozzi, S., Pelletier, J. and Nadon, R. (2006) Statistical practice in high-throughput screening data analysis, Nature Biotechn 24(2), 167–175.
medpolish
,
plotSpatialEffects
,
normalizePlates
,
summarizeChannels
1 2 3 4 5 6 | data(KcViabSmall)
x <- KcViabSmall
x <- Bscore(x, save.model = TRUE)
## identical result, but calling Bscore function from "normalizePlates"
xopt <- normalizePlates(x, normalizationMethod="Bscore", save.model = TRUE)
all(x$xnorm==xopt$xnorm, na.rm=TRUE)
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.