Oocyte {pda}R Documentation

Oocyte Development

Description

Rose-Hellekant and Bavister (1996) has been studying the chemistry of oocyte (egg) development. In one experiment, she examined the effect of two agents, forskolin and h89.

Usage

data(Oocyte)

Format

Oocyte data frame with 192 observations on 8 variables.
[,1] fors factor forskolin level
[,2] h89 factor H89 level
[,3] date factor date
[,4] dup factor duplicate
[,5] toocytes numeric toocytes
[,6] gv numeric gv
[,7] mi numeric mi

Source

Terry Rose-Hellekant

References

Rose-Hellekant TA and Bavister BD (1996) `Roles of protein kinase A and C in spontaneous maturation and in forskolin or 3-isobutyl-1-methylxanthine maintained meiotic arrest of bovine oocytes', Molecular Reproduction & Development 44, 241-249.

Examples

data( Oocyte )

Oocyte$asper <- 100 * asin( sqrt( Oocyte$gv / Oocyte$toocytes ) )

Oocyte$h89 <- ordered( Oocyte$h89 )
Oocyte$fors <- ordered( Oocyte$fors )
Oocyte$date <- ordered( Oocyte$date )

sample.size( Oocyte$h89, Oocyte$fors )

cat( "Type I sums of squares:\n" )
Oocyte.fit <- aov( asper ~ h89 * fors, Oocyte )
summary( Oocyte.fit )
summary( aov( asper ~ fors * h89, Oocyte))
cat( "Type III sums of squares:\n" )
drop1( Oocyte.fit, formula( Oocyte.fit ), test = "F" )

cat( "Additive model:\n" )
Oocyte.afit <- aov( asper ~ h89 + fors, Oocyte )
cat( "Type II sums of squares:\n" )
drop1( Oocyte.afit, formula( Oocyte.afit ), test = "F" )

# D:10.1 Oocyte additive and interactive models

lsd.plot( Oocyte.afit, factors = c("fors","h89"),
  xlab = "(a) additive fit", ylab = "fors",
  more = TRUE, split = c(1,1,2,2) )
margin.plot( Oocyte.afit, factors = c("fors","h89"),
  xlab = "(b) additive margin", ylab = "",
  more = TRUE, split = c(2,1,2,2) )
lsd.plot( Oocyte.fit, factors = c("fors","h89"),
  xlab = "(c) interactive fit", ylab = "fors",
  more = TRUE, split = c(1,2,2,2) )
margin.plot( Oocyte.fit, factors = c("fors","h89"),
   xlab = "(d) interactive margin", ylab = "",
  split = c(2,2,2,2) )

# D:10.2 Oocyte Effects Plot
effect.plot( Oocyte.fit,
  main = "Figure D:10.2 Oocyte Effects Plot" )

cat( "Cautionary tale on Type III sums of squares\n",
   "Be sure to have sum to zero contrasts!\n" )
# first alter contrasts for H89
contrasts( Oocyte$h89 )
contrasts( Oocyte$h89 ) <- contr.treatment
contrasts( Oocyte$h89 )
Oocyte.trt <- aov( asper ~ h89 * fors, Oocyte )
drop1( Oocyte.trt, formula( Oocyte.trt ), test = "F" )

# now alter contrasts for forskolin
contrasts( Oocyte$fors )
contrasts( Oocyte$fors ) <- contr.treatment
contrasts( Oocyte$fors )
Oocyte.trt <- aov( asper ~ h89 * fors, Oocyte)
drop1( Oocyte.trt, formula( Oocyte.trt ), test = "F" )

# resetting contrasts for your sanity
contrasts( Oocyte$h89 ) <- contr.poly
contrasts( Oocyte$fors ) <- contr.poly

[Package pda version 1.2-2 Index]