Description Usage Arguments Details Value Author(s) References See Also
Estimate the meanvariance relationship and use this to compute appropriate observationallevel weights.
1 2 3 4 
y 
a numeric 
design 
design matrix with rows corresponding to samples and columns to coefficients to be estimated. Defaults to the unit vector meaning that samples are treated as replicates. 
block 
vector or factor specifying a blocking variable on the arrays. Has length equal to the number of arrays. 
correlation 
intrablock correlation 
span 
width of the smoothing window, as a proportion of the data set. 
plot 

group 
categorical vector or factor giving group membership of columns of 
col 
vector of colors for plotting group trends 
lwd 
line width for plotting group trends 
pch 
plotting character. Default is integer code 16 which gives a solid circle. If a vector, then should be of length 
cex 
numeric vector of plot symbol expansions. If a vector, then should be of length equal to number of groups. 
alpha 
transparancy of points, on scale from 
legend 
character string giving position to place legend. 
vooma
is an acronym for meanvariance modelling at the observational level for arrays.
vooma
estimates the meanvariance relationship in the data, and uses this to compute appropriate weights for each observation.
This done by estimating a meanvariance trend, then interpolating this trend to obtain a precision weight (inverse variance) for each observation.
The weights can then used by other functions such as lmFit
to adjust for heteroscedasticity.
voomaByGroup
estimates precision weights separately for each group. In other words, it allows for different meanvariance curves in different groups.
An EList object with the following components:
E 
numeric matrix of as input 
weights 
numeric matrix of weights 
design 
numeric matrix of experimental design 
genes 
dataframe of gene annotation, only if 
Charity Law and Gordon Smyth
Law, C. (2013). Precision weights for gene expression analysis. PhD Thesis. University of Melbourne, Australia. http://repository.unimelb.edu.au/10187/17598
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