Description Usage Arguments Details Value Author(s) References Examples
Batch effect is corrected by subtracting its effect in the affected dimensions or PCs. Both corrected and uncorrected dimensions are then used to predict the data.
1 | correctBatch(res11, designX, Ys, batchCL, ngrps, grps, Conf, nt, cGsub, comres, theme, type)
|
res11 |
Results of fitting the PPCCA model. |
designX |
Design matrix for the covariates |
Ys |
Expression data |
batchCL |
A vector identifying batches. |
ngrps |
Number of batches |
grps |
Batches |
Conf |
A vector identifying biological classes. |
nt |
Number of biological classes |
cGsub |
Colors |
comres |
Results of ComBat correction |
theme |
ggplot theme |
type |
Plot |
Batch effect is corrected by subtracting its effect only in the affected dimensions or PCs. Both the corrected and uncorrected dimensions are then used to predict the data.
Results in correctBatch folder in the working directory.
Nyamundanda, G., Poudel, P., Patil, Y. and Sadanandam, A.
Nyamundanda, G., Poudel, P., Patil, Y. and Sadanandam, A., 2017. A novel and robust statistical method to diagnose and correct batch effects in genomic data.
1 2 3 | ##---- Should be DIRECTLY executable !! ----
##-- ==> Define data, use random,
##-- or do help(data=index) for the standard data sets.
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