scripts/20bExpression-for-variety.Rnw

Version 1

% -*- TeX:Rnw:UTF-8 -*-
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% .R knitr file  ************************************************
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###############################################
##                                           ##
## (c) Andrej Blejec (andrej.blejec@nib.si)  ##
##                                           ##
###############################################
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<<echo=FALSE,results='hide'>>=
options(width=70)
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\section{Analysis for variety}

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var <- "C"
select <- pd$variety == var
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design <- with(pd[select,], model.matrix(~ treat* day))
head(design)
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fit <- lmFit(exprs[ ,select], design)
fit <- eBayes(fit)
head(fit1[1:6,])
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my.interaction.plot <- function(F1,F2,y,...){
    xlab <- deparse(substitute(F1))
    y <- unlist(y)
    ylim <- range(y)
    interaction.plot(F1, F2, y,
     col = 1:length(levels(F2)),
     xlab = xlab,
     ylim = ylim,
     type = "b",
     pch = rep(16, length(levels(F2))),
     ...
     )
    points(as.numeric(F1)+(as.numeric(F2)-1.5)/15,y, col=as.numeric(F2))
    }
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tt <- topTable(fit, coef=4)
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varname <- rownames(tt)[1]
with(pd[select, ], my.interaction.plot(day,treat,exprs[varname,select]) )
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