这个细节，是转换坐标轴上文字的方向，虽然是很小的问题，也花费了一些时间，惭愧。
方案：
1. from ky

pdf("after-normalization.pdf",width=4+dim(data2)[[2]]/5,height=6)

palette(c("#dfeaf4","#f4dfdf","#AABBCC"))

par(mar=c(2+round(max(nchar(sampleNames(data)))/2),4,2,1))

title <- paste ("GSE32676"," afternormailization", sep ='')

boxplot(data2, boxwex=0.6, notch=T, main=title, outline=FALSE,las=2, col=fl)

legend("topleft", labels, fill=palette(),bty="n")

dev.off()

2. from GEO
# Version info: R 2.14.1, Biobase 2.15.3, GEOquery 2.23.2, limma 3.10.1# R scripts generated Wed Sep 4 06:00:01 EDT 2013# Unable to generate script analyzing differential expression.# Invalid input: at least two groups of samples should be selected.################################################################# Boxplot for selected GEO sampleslibrary(Biobase)library(GEOquery)# load series and platform data from GEOgset <- getGEO("GSE14407", GSEMatrix =TRUE)if (length(gset) > 1) idx <- grep("GPL570", attr(gset, "names")) else idx <- 1gset <- gset[[idx]]# set parameters and draw the plotdev.new(width=4+dim(gset)[[2]]/5, height=6)par(mar=c(2+round(max(nchar(sampleNames(gset)))/2),4,2,1))title <- paste ("GSE14407", '/', annotation(gset), " selected samples", sep ='')boxplot(exprs(gset), boxwex=0.7, notch=T, main=title, outline=FALSE, las=2)legend("topleft", labels, fill=palette(), bty="n")

3. from mine

> pdf("Before Normalization.pdf",width=6,height=6)
> title <- paste ("GSE14407"," before normailization", sep ='')
> palette(c("#dfeaf4","#f4dfdf", "#AABBCC"))
> par(mar=c(2+round(max(nchar(sampleNames(data)))/2),4,2,1))
> boxplot(data,boxwex=0.6, notch=T, main=title, outline=FALSE, las=2, col=c("mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","blue","blue","blue","blue","blue","blue","blue","blue","blue","blue","blue","blue"))
> legend("topleft", labels, fill=palette(), bty="n")
Error in as.graphicsAnnot(legend) :
argument "legend" is missing, with no default
> dev.off()

> pdf("After Normalization.pdf",width=6,height=6)
> title <- paste ("GSE14407"," after normailization", sep ='')
> par(mar=c(2+round(max(nchar(sampleNames(data)))/2),4,2,1))
> boxplot(mydata,boxwex=0.6, notch=T, main=title, outline=FALSE, las=2, col=c("mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","mediumturquoise","blue","blue","blue","blue","blue","blue","blue","blue","blue","blue","blue","blue"))
> legend("topleft", labels, fill=palette(), bty="n")
Error in as.graphicsAnnot(legend) :
argument "legend" is missing, with no default
> dev.off()
pdf
2

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