scaleNormMultCont {SCnorm} | R Documentation |
After conditions are independently normalized with the count-depth effect removed, conditions need to be additionally scaled prior to further analysis. Genes that were normalized in both conditions are split into quartiles based on their un-normalized non-zero medians. Genes in each quartile are scaled to the median fold change of condition specific gene means and overall gene means.
scaleNormMultCont(NormData, OrigData, Genes, useSpikes, useZerosToScale)
NormData |
list of matrices of normalized expression counts and scale factors for each condition. Matrix rows are genes and columns are samples. |
OrigData |
list of matrices of un-normalized expression counts. Matrix rows are genes and columns are samples. Each item in list is a different condition. |
Genes |
vector of genes that will be used to scale conditions, only want to use genes that were normalized. |
useSpikes |
whether to use spike-ins to perform between condition scaling (default=FALSE). Assumes spike-in names start with "ERCC-". |
useZerosToScale |
whether to use zeros when scaling across conditions (default=FALSE). |
matrix of normalized and scaled expression values for all conditions.
Rhonda Bacher