positiveControl: Acessor functions for the 'positiveControl' slot in a...
In Shedimus/NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
nCounter Analyzer has positive spike-in RNA hybridization controls
for each sample which can be used to estimate the overall efficiency
of hybridization and recovery for each sample.
Usage
1
2
3
4
## S4 method for signature 'NanoStringSet'
positiveControl(object)
## S4 replacement method for signature 'NanoStringSet,matrix'
positiveControl(object) <- value
Arguments
object
A NanoStringSet object.
value
A matrix with six positive control genes.
Details
Positive control genes are provided by NanoString nCounter technology.
For each sample, nCounter provide six positive controls corresponding
to six different concentrations in the 30 ul hybridzation:
128fM, 32fM, 8fM, 2fM, 0.5fM, and 0.125fM. Six positive control genes must
be order by concentrations from high to low.
Value
A matrix contain positive control genes
Author(s)
Hong Wang <hong.wang@uky.edu>
chi wang <chi.wang@uky.edu>
See Also
positiveFactor
Examples
1
2
3
4
5
6
7
8
9
data(NanoStringData)
## obtain positive control genes
positiveControl(NanoStringData)
## assign a matrix
n=ncol(exprs(NanoStringData))
x=matrix(c(128,32,8,2,0.5,0.125)*80,ncol=1)
positive=matrix(rpois(6*n,x),ncol=n)
positiveControl(NanoStringData)=positive
Shedimus/NanoStringDiff documentation built on Dec. 5, 2019, 1:56 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Description Usage Arguments Details Value Author(s) See Also Examples
Description
nCounter Analyzer has positive spike-in RNA hybridization controls for each sample which can be used to estimate the overall efficiency of hybridization and recovery for each sample.
Usage
1 2 3 4 | ## S4 method for signature 'NanoStringSet'
positiveControl(object)
## S4 replacement method for signature 'NanoStringSet,matrix'
positiveControl(object) <- value
|
Arguments
object |
A NanoStringSet object. |
value |
A matrix with six positive control genes. |
Details
Positive control genes are provided by NanoString nCounter technology. For each sample, nCounter provide six positive controls corresponding to six different concentrations in the 30 ul hybridzation: 128fM, 32fM, 8fM, 2fM, 0.5fM, and 0.125fM. Six positive control genes must be order by concentrations from high to low.
Value
A matrix contain positive control genes
Author(s)
Hong Wang <hong.wang@uky.edu> chi wang <chi.wang@uky.edu>
See Also
positiveFactor
Examples
1 2 3 4 5 6 7 8 9 | data(NanoStringData)
## obtain positive control genes
positiveControl(NanoStringData)
## assign a matrix
n=ncol(exprs(NanoStringData))
x=matrix(c(128,32,8,2,0.5,0.125)*80,ncol=1)
positive=matrix(rpois(6*n,x),ncol=n)
positiveControl(NanoStringData)=positive
|
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.