housekeepingControl: Acessor functions for the 'housekeepingControl' slot in a...
In tingtina/NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
user-defined housekeeping control genes can be used to estimate housekeeping
factors to adjust variation caused by different sample input.
Usage
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## S4 method for signature 'NanoStringSet'
housekeepingControl(object)
## S4 replacement method for signature 'NanoStringSet,matrix'
housekeepingControl(object) <- value
Arguments
object
A NanoStringSet object.
value
A matrix with housekeeping control genes.
Details
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.
Value
A matrix contain housekeeping control genes
Author(s)
Hong Wang <hong.wang@uky.edu>
chi wang <chi.wang@uky.edu>
See Also
housekeepingFactor
Examples
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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
tingtina/NanoStringDiff documentation built on May 24, 2019, 10 p.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
user-defined housekeeping control genes can be used to estimate housekeeping factors to adjust variation caused by different sample input.
Usage
1 2 3 4 | ## S4 method for signature 'NanoStringSet'
housekeepingControl(object)
## S4 replacement method for signature 'NanoStringSet,matrix'
housekeepingControl(object) <- value
|
Arguments
object |
A NanoStringSet object. |
value |
A matrix with housekeeping control genes. |
Details
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.
Value
A matrix contain housekeeping control genes
Author(s)
Hong Wang <hong.wang@uky.edu> chi wang <chi.wang@uky.edu>
See Also
housekeepingFactor
Examples
1 2 3 4 5 6 7 8 9 | 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
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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