housekeepingFactor: Acessor functions for the 'housekeepingFactor' slot in a...
In Shedimus/NanoStringDiff: Differential Expression Analysis of NanoString nCounter Data
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
Housekeeping size factors can be used to adjust the variance
caused by different sample input.
Usage
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## S4 method for signature 'NanoStringSet'
housekeepingFactor(object)
## S4 replacement method for signature 'NanoStringSet,numeric'
housekeepingFactor(object) <- value
Arguments
object
A NanoStringSet object.
value
A vector of housekeeping size factors.
Details
Housekeeping gene normalization corrects for different in sample input
between assays,since reference genes are suppose have same expression
rate between samples.So the read counts from housekeeping genes, after
subtracting background noise and adjusting by positive size factors,
that are not expected to vary between samples. If there exist difference,
which should be caused by sample input variation.
Value
A vector contain housekeeping factors
Author(s)
Hong Wang <hong.wang@uky.edu>
chi wang <chi.wang@uky.edu>
See Also
housekeepingControl
Examples
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7
data(NanoStringData)
## obtain housekeeping factors
housekeepingFactor(NanoStringData)
## assign a vector
n=ncol(exprs(NanoStringData))
housekeepingFactor(NanoStringData)=rep(1,n)
Shedimus/NanoStringDiff documentation built on Dec. 5, 2019, 1:56 a.m.
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
Housekeeping size factors can be used to adjust the variance caused by different sample input.
Usage
1 2 3 4 | ## S4 method for signature 'NanoStringSet'
housekeepingFactor(object)
## S4 replacement method for signature 'NanoStringSet,numeric'
housekeepingFactor(object) <- value
|
Arguments
object |
A NanoStringSet object. |
value |
A vector of housekeeping size factors. |
Details
Housekeeping gene normalization corrects for different in sample input between assays,since reference genes are suppose have same expression rate between samples.So the read counts from housekeeping genes, after subtracting background noise and adjusting by positive size factors, that are not expected to vary between samples. If there exist difference, which should be caused by sample input variation.
Value
A vector contain housekeeping factors
Author(s)
Hong Wang <hong.wang@uky.edu> chi wang <chi.wang@uky.edu>
See Also
housekeepingControl
Examples
1 2 3 4 5 6 7 | data(NanoStringData)
## obtain housekeeping factors
housekeepingFactor(NanoStringData)
## assign a vector
n=ncol(exprs(NanoStringData))
housekeepingFactor(NanoStringData)=rep(1,n)
|
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.
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