Dear all,
I'd appreciate your input if you could.
I first normalized data, and it is called john2. We are interested in Notch
signaling
pathway and want to get the expression values for all genes on this pathway.
So
I tried the below (it does not look neat...sorry that I am new to R coding):

######KEGG:Notch#####################
######http://www.genome.ad.jp/kegg/pathway/hsa/hsa04330.html######
Notch<-mget("04330",lumiHumanAllPATH2PROBE,ifnotfound = NA)
write.table(Notch, file="Notch.txt",quote=FALSE,row.names=FALSE,col.names =
FALSE)
Notch1<-read.table('Notch.txt',header=FALSE)
Notch_geneSymbol <- getSYMBOL(as.vector(Notch1[,1]), 'lumiHumanAll.db')

########Retrieve the normalized data#########
dataMatrix <- exprs(john2)
probeList <- rownames(dataMatrix)
geneSymbol <- getSYMBOL(probeList, 'lumiHumanAll.db')
anno<-data.frame(dataMatrix,geneSymbol=geneSymbol)

########Subset expression data for Notch genes#######
b<-anno[as.vector(Notch1[,1]),]
dim(b)


You will see many empty rows in b filled with "NA". I wonder what
the reason could be.

Thank you so much!


Allen


> b[1:10,1:3]
                      X451Lu X451Lu885 geneSymbol
NA                        NA        NA       <NA>
QeUV54t73rDarMMp3k  9.220161  9.577290       JAG1
NqbdUs8V6OMoPh1puQ 10.386946 10.960459     CREBBP
Te17_XV.gA5S4QmAUE  8.250515  8.325535     CREBBP
KghpNGCSdQCgCfqa5U 10.038218  9.930820      CTBP1
TnYhDwobqOKdYhKGa8  9.509115  9.382045      CTBP1
NA.1                      NA        NA       <NA>
iAW0JWKaMiFGUuFL7I  8.724987  8.597907      CTBP1
NA.2                      NA        NA       <NA>
NA.3                      NA        NA       <NA>

> Notch_geneSymbol[1:10]
QTei90CF6p57gnoHmo QeUV54t73rDarMMp3k NqbdUs8V6OMoPh1puQ Te17_XV.gA5S4QmAUE
            "JAG1"             "JAG1"           "CREBBP"           "CREBBP"
KghpNGCSdQCgCfqa5U TnYhDwobqOKdYhKGa8 f2IQ8KG6jinWIShmvc iAW0JWKaMiFGUuFL7I
           "CTBP1"            "CTBP1"            "CTBP1"            "CTBP1"
NpkSqRU027UU5_RSBQ K3FQQYgKWgrnmnnTRo
           "CTBP2"             "DTX1"
>

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