Reformats raw Ct data for geNorm analysis (non-parametric selection of stable control genes) as implemented in selectHKgenes function (package SLqPCR)

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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

1
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

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