housekeepingControl {NanoStringDiff} | R Documentation |
user-defined housekeeping control genes can be used to estimate housekeeping factors to adjust variation caused by different sample input.
## S4 method for signature 'NanoStringSet' housekeepingControl(object) ## S4 replacement method for signature 'NanoStringSet,matrix' housekeepingControl(object) <- value
object |
A NanoStringSet object. |
value |
A matrix with housekeeping control genes. |
NanoString nCounter analyzer also contains probes for a set of species-specific mRNA housekeeping(reference) genes that are not spike-in the system. Nanostring recommends at least three housekeeping genes, but the more that are included, the more accurate the normalization will be. Housekeeping control genes are expected consistent in their expression levels.
A matrix contain housekeeping control genes
Hong Wang <hong.wang@uky.edu> chi wang <chi.wang@uky.edu>
housekeepingFactor
data(NanoStringData) ## obtain housekeeping control genes housekeepingControl(NanoStringData) ## assign a matrix n=ncol(exprs(NanoStringData)) r=nrow(housekeepingControl(NanoStringData)) housekeeping=matrix(rpois(r*n,1000),ncol=n) housekeepingControl(NanoStringData)=housekeeping