badCt:
Evaluation of the qPCR technical replicates
Description
This function allows you to evaluate your qPCR technical replicates, you only
need to define the threshold (according to Hellemans et al. (2007), 0.5 is a
good threshold value), the dataset and the number of technical replicates you
have done. I recommand you to use the gWidgets package to easily exclude the
failed replicates.
Usage
badCt(data, r, threshold, na.rm = FALSE)
Arguments
data
data.frame containing row datas (genes in columns, samples in rows, Cq values).
r
numeric, number of qPCR replicates.
threshold
numeric, the maximal variation between your qPCR replicates.
na.rm
a logical value indicating whether NA values should be stripped before the
computation proceeds.
Value
This function returns the position (sample position and column position) where
the variation between qPCR replicates is superior to the threshold value.
Details
To facilitate the use of the function, I suggest you to use the gWidgets package
as described in the vignette.
References
Jan Hellemans, Geert Mortier, Anne De Paepe, Frank Speleman and Jo Vandesompele.
qBase relative quantification framework and software for management and
automated analysis of real-time quantitative PCR data. Genome Biology 2007,
8:R19 (doi:10.1186/gb-2007-8-2-r19).
