Dear Christian,

I read your vignette Ť Introduction to the xps Package: Comparison to 
Affymetrix Power Tools ť and I tried to compare 2 gene expression 
arrays : U133 Plus 2 andHuman Gene ST 1.

I followed your R instructions in the script "script4bestmatch.R". But I 
noticed something strange in my output.

I downloaded "U133PlusVsHuGene_BestMatch.txt" in Affymetrix website.

My instructions are :

#Function "uniqueframe"

uniqueframe <- function(ma) {

maxunique <- function(id, m) {

m <- m[which(m[,1] == id),];

m <- m[which(m[,2] == max(m[,2])),];

return(m[1,]);

}

dup <- duplicated(ma[,1])

uni <- unique(ma[dup,1])

ds <- NULL

for (i in uni) {ds <- rbind(ds, maxunique(i,ma))}

tmp <- ma[dup==F,]

ds <- rbind(ds, tmp)

ds <- ds[order(rownames(ds)),]

return(ds)

}

# Importation of "U133PlusVsHuGene_BestMatch.txt"

up2hg<-read.delim("D:/Naima/CancerMoelleOsseuse_EFS/Analyse_Package_XPS/U133PlusVsHuGene_BestMatch.txt",row.names=3,comment.char="")

dim(up2hg)

[1] 2912919

up2hg<-up2hg[,5:6]

up2hg_cor<-uniqueframe(up2hg)

colnames(up2hg_cor)<-c("HuGene","PercentU2G")

dim(up2hg_cor)

[1] 252512

  write.csv2(up2hg_cor,"D:/Naima/CancerMoelleOsseuse_EFS/Outputs/Probesets_U133PlusVsHuGene.csv")

The initial data frame "up2hg" contains 29 129 lines and when I do the 
instruction "uniqueframe", the data frame obtaining is composed of 25251 
lines. But the number of unique probesets for human Gene array is 17984.

When I see the output (Probesets_U133PlusVsHuGene.csv), there is 
something strange:

For example:

  U1332P

	

HuGene

	

PercentU2G

1552257_a_at

	

8076569

	

99,41

1552257_a_at1

	

8076569

	

99,41

1552264_a_at

	

8074791

	

98,42

1552264_a_at1

	

8074791

	

98,42

There is still duplicated probesets in HuGene probesets and new 
probesets in U1332P are created "1552257_a_at1".

I've done something wrong?

Thank you for your help.

Naďma


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