| cq2genorm {MCMC.qpcr} | R Documentation |
Reformats raw Ct data for geNorm analysis (non-parametric selection of stable control genes) as implemented in selectHKgenes function (package SLqPCR)
Description
Does similar procedures as cq2log, but in the end converts the data into relative expression values, leaves it unstacked, and removes factor columns.
Usage
cq2genorm(data, genes, effic, noamp=38)
Arguments
data |
raw qRT-PCR data; see help for cq2counts for details on formatting |
genes |
Vector of names of the potential control genes. Make sure you select only the potential control genes for this analysis, otherwise geNorm might prefer actual responsive genes if they co-vary and have very low variance. |
effic |
PCR efficiency data for each of the analyzed genes; see help for cq2counts for details on formatting. |
noamp |
what to do about Ct values '-1', denoting no amplification. By default, these will be assigned an arbitrarily low expression value corresponding to slightly less than one molecule. Specify 'noamp=NA' if you want to skip samples containing any of these. |
Details
See cq2counts help page for details.
Value
A dataset to be fed into the function selectHKgenes (package SLqPCR).
Author(s)
Mikhail V. Matz, UT Austin
References
Matz MV, Wright RM, Scott JG (2013) No Control Genes Required: Bayesian Analysis of qRT-PCR Data. PLoS ONE 8(8): e71448. doi:10.1371/journal.pone.0071448