Merge two data frames and order according to a column...

find_annotations_for_non_overlaping_probes <- function
(probeList, annotations, expressedList1) {

annotationIdx <- match(probeList, annotations[,1])
pvalueIdx1 <- match (probeList, expressedList1[,4])

id1 <- as.data.frame(expressedList1[pvalueIdx1,])
id3 <- as.data.frame(annotations[annotationIdx,])

rownames (id1) <- probeList ;
colnames(id1) <- c("rawp", "adjp", "index", "probeId")
rownames (id3) <- probeList

resultOut <- data.frame(merge(id1, id3, by = "row.names"), row.names = 1)
resultOut.sorted <- resultOut[do.call(order, resultOut[1]),]
}

Writing R-plots into different devices

pdf("foo.pdf")

plot(x)
dev.off()

Other possibilities are jpeg(), tiff(), postscript() etc.

Setting up aroma.affymetrix for analysis

Setting up aroma.affymetrix for analysis two directories : rawData and annotationData
from where aroma is launched

rawData/cancer_name/HuGene-1_0-st-v1/*.CEL
annotationData/chipTypes/HuGene-1_0-st-v1/*.cdf
annotationData/chipTypes/HuGene-1_0-st-v1/NetAffx/*.csv