EF1data<-read.table("EF1.csv", sep=",", header=T)
getwd()
setwd("/Users/emmatimminsschiffman")
getwd()
EF1data<-read.table("EF1.csv", sep=",", header=T)
EF1.anova<-lm(Ct~Replicate, data=EF1data)
EF1var<-anova(EF1.anova)
TukeyHSD(EF1var, ordered=T, conf.level=0.95)
EF1var
setwd("/Users/emmatimminsschiffman/Documents/Autumn 2009/Stats")
data<-read.table("HW4.csv", sep=",",header=TRUE)#
grass.anova<-lm(Density~Treatment, data=data)
setwd("/Users/emmatimminsschiffman")
data<-read.table("HW4.csv", sep=",",header=TRUE)#
grass.anova<-lm(Density~Treatment, data=data)
grassvar<-anova(grass.anova)
grassvar
EF1data<-read.table("EF1.csv", sep=",", header=T)
EF1.anova<-lm(Ct~Replicate, data=EF1data)
EF1var<-anova(EF1.anova)
EF1var
TukeyHSD(EF1var, ordered=T, conf.level=0.95)
?TukeyHSD
?subset
subEF1<-subset(EF1data, Replicate==c("First", "Second", "Third"))
EF1.anova<-lm(Efficiency~Replicate, data=EF1data)
EF1var<-anova(EF1.anova)
EF1var
Prxdata<-read.table("Prx6.csv", sep=",", header=T)
Prx.anova<-lm(Ct~Replicate, data=Prxdata)
Prxvar<-anova(Prx.anova)
Prxvar
TukeyHSD(Prxvar, ordered=F, conf.level=0.95)
Prxdata<-read.table("Prx6.csv", sep=",", header=T)
Prxco2<-lm(Ctco2~Replicate, data=Prxdata)
Prxvar1<-anova(Prxco2)
Prxvar1
TukeyHSD(Prxvar1, ordered=F, conf.level=0.95)
TukeyHSD(Prxvar1, ordered=T, conf.level=0.95)
PrxC<-lm(CtC~Replicate, data=Prxdata)
Prxvar2<-anova(PrxC)
Prxvar2
Prxnew<-read.table("Prx6new.csv", sep=",", header=T)
Prxco2.2<-lm(Ctco2~Replicate, data=Prxnew)
Prxvar1.2<-anova(Prxco2.2)
Prxvar1.2
Prxnew<-read.table("Prx6new.csv", sep=",", header=T)
Prxco2.2<-lm(Ctco2~Replicate, data=Prxnew)
Prxvar1.2<-anova(Prxco2.2)
Prxvar1.2
HIFdata<-read.table("HIF.csv", sep=",", header=T)
HIFco2<-lm(Ctco2~Replicate, data=HIFdata)
HIFvar1<-anova(HIFco2)
HIFvar1
HIFC<-lm(CtC~Replicate, data=HIFdata)
HIFvar2<-anova(HIFC)
HIFvar2
HIFdata.2<-read.table("HIFnew.csv", sep=",", header=T)
HIFco2.2<-lm(Ctco2~Replicate, data=HIFdata.2)
HIFvar1.2<-anova(HIFco2.2)
HIFvar1.2
HIFdata.2<-read.table("HIFnew.csv", sep=",", header=T)
HIFco2.2<-lm(Ctco2~Replicate, data=HIFdata.2)
HIFvar1.2<-anova(HIFco2.2)
HIFvar1.2
HIFC.2<-lm(CtC~Replicate, data=HIFdata.2)
HIFvar2.2<-anove(HIFC.2)
HIFvar2.2<-anova(HIFC.2)
HIFvar2.2
?read
?read.csv
help.search("export")
help.search("file")
?write
getwd()
?unique
?subset
sub.Geneasso<-data.frame(a=c(1,1,1), b=c(2,2,2), c=c(3,3,3,3), d=c(4,4,4), e=c(5,5,5), f=c(6,6,6), g=c(7,7,7), h=c(8,8,8), i=c(9,9,9))
sub.Geneasso<-data.frame(a=c(1,1,1), b=c(2,2,2), x=c(3,3,3,3), d=c(4,4,4), e=c(5,5,5), f=c(6,6,6), g=c(7,7,7), h=c(8,8,8), i=c(9,9,9))
sub.Geneasso<-data.frame(a=c(1,1,1), b=c(2,2,2), x=c(3,3,3), d=c(4,4,4), e=c(5,5,5), f=c(6,6,6), g=c(7,7,7), h=c(8,8,8), i=c(9,9,9))
sub.Geneasso
final.data<-subset(sub.Geneasso, select=sub.Geneasso[,1]:sub.Geneasso[,5]&sub.Geneasso[,8])
final.data<-subset(sub.Geneasso, select=sub.Geneasso[,1]:sub.Geneasso[,5])
final.data
?cbind
cbind(final.data, sub.Geneass[,8])
cbind(final.data, sub.Geneasso[,8])
is.dataframe(final.data)
is.data.frame(final.data)
cbind(sub.Geneasso[,1],sub.Geneasso[,2],sub.Geneasso[,3],sub.Geneasso[,4],sub.Geneasso[,5],sub.Geneasso[,8])
getwd()
data<-read.csv("data")
data<-read.csv("data.csv")
sub.data<-subset(data, select=data[,1]:data[,5])
sub.data
ncol(data)
cbind(data[,1], data[,2], data[,3], data[,4], data[,5], data[,8])
as.list(cbind(data[,1], data[,2], data[,3], data[,4], data[,5], data[,8]))
new.data<-data.frame(cbind(data[,1], data[,2], data[,3], data[,4], data[,5], data[,8]))
new.data
dat
data
help.search("delete column")
help.search("remove column")
help.search("colum")
data[,1]
is.factor(data[,1])
is.numeric(data.[,1])
is.numeric(data[,1])
?text
data[c(1,2,3,4,5,8),]
ncol(data)
new.data<-data.frame(data[c(1,2,3,4,5,8),], ncol=6)
new.data
new.data<-data.frame(data[c(1,2,3,4,5,8),])
new.data
new.data<-data.frame(data[,c(1,2,3,4,5,8)])
new.data
?pdf
x<-(1, times=10)
x<-(1, n=10)
x<-c(1,1,1,1,1,1,1,1,1,1,1)
y<-c(4,4,4,4,4,4,4,4,4,4,4)
plot(x)
lines=y
rm(lines)
?plot
lines(y)
plot(x)
x<-c(1,1,1,1,1,1,1,1,1,1,1)
plot(x)
lines(y=c(0:1.4,11), x2=c(4,4,4,4,4,4,4,4,4,4,4))
lines(y=c(0.6,0.7,0.8,.9,1,1.1,1.2,1.3,1.4), x2=c(4,4,4,4,4,4,4,4,4,4,4))
?lines
lines(x2=c(4,4,4,4,4,4,4,4,4,4,4),y=c(0.6,0.7,0.8,.9,1,1.1,1.2,1.3,1.4))
yvalues<-c(1750, 2010, 2050, 2100)
xvalues<-c(270, 370, 500, 850)
?par
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="7")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="c")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="u")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="]")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="c")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=3)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=2)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.75)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.75, cex.main=2)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.75, cex.main=1/75)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.75, cex.main=1.75)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.75, cex.main=1.5)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.5, cex.main=1.5)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.5, cex.main=1.5, cex.lab=1.25)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.5, cex.main=2, cex.lab=1.25, col.lab="steelblue4", lty="dashed", pty="m")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.5, cex.main=1.5, cex.lab=1.25, col.lab="steelblue4", lty="dashed", pty="m")
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.5, cex.main=1.5, cex.lab=1.25, col.lab="steelblue4", lty="dashed", lwd=2)
plot(yvalues, xvalues, xlab="Year", ylab="Estimate of atmospheric CO2 (ppm)", type="b", main="IPCC (2007) Projected Estimates of Atmospheric CO2", bty="l", cex=2, cex.axis=1.5, cex.main=1.5, cex.lab=1.25, col.lab="steelblue4", lty="dashed", lwd=2, col.main="navyblue")
getwd()
setwd("/Users/emmatimminsschiffman/Documents/Dissertation/Analysis/Expression analysis adult oysters")
adults<-read.csv("ANOVA-CO2.csv", sep=",", header=T)
Prx6AC<-mean(adults$Prx6[1:8])#
Prx6AV<-mean(adults$Prx6[9:16])#
Prx6CC<-mean(adults$Prx6[17:24])#
Prx6CV<-mean(adults$Prx6[25:32])
plotprx6<-c(Prx6AC,Prx6AV,Prx6CC,Prx6CV)
barprx<-barplot(plotprx6, col="violet", main="Prx6 Expression in Adult C. gigas", xlab="Treatment", ylab="Normalized Expression Value", names.arg=c("AC", "AV", "CC", "CV"), axes=TRUE, xpd=FALSE, ylim=c(0,1.2), cex.main=1.5)
barprx<-barplot(plotprx6, col="violet", main="Prx6 Expression in Adult C. gigas", xlab="Treatment", ylab="Normalized Expression Value", names.arg=c("AC", "AV", "CC", "CV"), axes=TRUE, xpd=FALSE, ylim=c(0,1.2), cex.main=2)
barprx<-barplot(plotprx6, col="violet", main="Prx6 Expression in Adult C. gigas", xlab="Treatment", ylab="Normalized Expression Value", names.arg=c("AC", "AV", "CC", "CV"), axes=TRUE, xpd=FALSE, ylim=c(0,1.2), cex.main=2, cex.lab=1.5)
barprx<-barplot(plotprx6, col="violet", main="Prx6 Expression in Adult C. gigas", ylab="Normalized Expression Value", names.arg=c("AC", "AV", "CC", "CV"), axes=TRUE, xpd=FALSE, ylim=c(0,1.2), cex.main=2, cex.lab=1.5)
barprx<-barplot(plotprx6, col="violet", main="Prx6 Expression in Adult C. gigas", ylab="Normalized Expression Value", names.arg=c("350 ppm", "350 ppm, +Vt", "970 ppm", "970 ppm, +Vt"), axes=TRUE, xpd=FALSE, ylim=c(0,1.2), cex.main=2, cex.lab=1.5)