Description Usage Arguments Value Author(s) References Examples
Normalize data to minimize the difference among the subgroups of the samples generated by experimental factor such as multiple plates (batch effects)
- the primary method is Multi-MA, but other fitting function, f in manuscript (e.g. loess) is available, too.
This method is based on the assumptions stated below
The geometric mean value of the samples in each subgroup (or plate) for a single target is ideally same as those from the other subgroups.
The subgroup (or plate) effects that influence those mean values for multiple observed targets are dependent on the values themselves. (intensity dependent effects)
1 2 |
mD |
a |
expGroup |
a |
represent_FUN |
a |
fitting_FUN |
|
isLog |
TRUE or FALSE, if the normalization should be conducted after log-transformation. The affinity proteomics data from suspension bead arrays is recommended to be normalized using the default, |
The data after normalization in a matrix
Mun-Gwan Hong <mun-gwan.hong@scilifelab.se>
Hong M-G, Lee W, Pawitan Y, Schwenk JM (201?) Multi-dimensional normalization of plate effects for multiplexed applications unpublished
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | data(sba)
B <- normn_MA(sba$X, sba$plate) # Multi-MA normalization
# MA-loess normalization
B <- normn_MA(sba$X, sba$plate, fitting_FUN= function(m_j, A) loess(m_j ~ A)$fitted)
# weighted linear regression normalization
B <- normn_MA(sba$X, sba$plate, fitting_FUN= function(m_j, A) {
beta <- lm(m_j ~ A, weights= 1/A)$coefficients
beta[1] + beta[2] * A
})
# robust linear regression normalization
if(any(search() == "package:MASS")) { # excutable only when MASS package was loaded.
B <- normn_MA(sba$X, sba$plate, fitting_FUN= function(m_j, A) {
beta <- rlm(m_j ~ A, maxit= 100)$coefficients
beta[1] + beta[2] * A
})
}
|
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.