Oocyte: Oocyte Development

In byandell/pda: Practial Data Analysis for Designed Experiments

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

byandell/pda documentation built on May 13, 2019, 9:27 a.m.