The non-parametric WILCOX_DDCt() function was added
to analyze the gene expression (ddCt method) using wilcox.test.
ANCOVA analysis which already was performed via the
analysisType = "ancova" argument of the
ANOVA_DDCt() function, now is performed using the
ANCOVA_DDCt() new function. The analysisType
argument was removed.
A function named compute_wDCt() was added which
cleans the data and computes weighted delta Ct (wDCt) values. Handling
missing data by this function has been described in the function
details.
Two arguments of the REPEATED_DDCt() function were
updated in order to be similar to those of the ANOVA_DDCt()
function: The repeatedFactor and
calibratorLevel arguments were changed to
mainFactor.column and mainFactor.level.order,
respectively.
The font size and legend position controls were added to the
efficiency() function.
It is now possible to return the lm formula that is used for
variance analysis in ANOVA_DDCt(), and
REPEATED_DDCt() functions using
object$perGene$gene_name$lm_formula command.
The rtpcr package now accepts any number of references and any number of target genes in a single analysis. The package computes the geometric mean of reference genes considering efficiency values.
Missing data can be denoted by NA in the input data frame. Values such as ‘0’ and ‘undetermined’ (for any E and Ct) are automatically converted to NA before passing to the downstream analysis. For target genes, NA for E or Ct measurements cause returning NA for the corresponding ΔCt for that replicate which is passed along to downstream statistical analyses. If there are more than one reference genes, NA in the place of the E or the Ct value of any reference gene cause skipping that reference gene and remaining genes are averaged in that replicate.
The long_to_wide() function was added to convert a
4-column qPCR data with long format to wide.
The last gene name in the plot output of the
TTEST_DDCt() function was fixed.