Teratogenesis rtPCR data — rtPCR • gplots

rtPCR data for experiments investigating a variety of markers for characterizing teratogenicity.

data(rtPCR)

Format

A data frame with 1672 observations on the following 21 variables.

PlateID: a factor with levels A0027002 through A0054019
Test.Substance: a factor with levels Compound A through Compound H
Teratogenicity.in.vivo: a factor with levels Non Strong Weak / Moderate
Sample: a factor with levels Sample 1 - Sample 152
Rep..: a factor with levels Rep 1 - Rep 21
Label: a factor with levels Ctrl, Neg. Ctrl P1 - P9, No Vehicle Ctrl, and Pos. Ctrl
Conc..ug.ml.: a numeric vector
Detector: a factor with levels ProbeType 1 - ProbeType 17
Avg.delta.Ct: a numeric vector
delta.Ct.SD: a numeric vector
delta.delta.Ct: a numeric vector
RQ: a numeric vector
X..RQ: a numeric vector
X100..Custom..: a numeric vector
X100...Custom..: a numeric vector
Custom..: a numeric vector
Custom...1: a numeric vector
RQ.Min: a numeric vector
RQ.Max: a numeric vector
Threshold: a numeric vector

Details

TBA

Source

Anonymized data.

Examples

data(rtPCR)

# same scale
overplot( RQ ~ Conc..ug.ml. | Test.Substance,
         data=rtPCR,
         subset=Detector=="ProbeType 7" & Conc..ug.ml. > 0,
         same.scale=TRUE,
         log="xy",
         f=3/4,
         main="Detector=ProbeType 7",
         xlab="Concentration (ug/ml)",
         ylab="Relative Gene Quantification"
         )


# different scales, but force lower limit to 0.01 
overplot( RQ ~ Conc..ug.ml. | Test.Substance,
         data=rtPCR,
         subset=Detector=="ProbeType 7" & Conc..ug.ml. > 0,
         log="xy",
         f=3/4,
         main="Detector=ProbeType 7",
         xlab="Concentration (ug/ml)",
         ylab="Relative Gene Quantification",
         min.y=0.01
         )