hi,

     I am working on two color 4x44Agilent array.I normalized the data with
Bioconductor,I used the following scripts to normalize the data.i want to
filterout the spots which are not good to be analysis across the array.how
can i filter the spots which are having the negative value after background
substraction.I want to do this befor normalization.

>limma(library)
> library(limma)
> targets_nod=readTargets("Both_negatv_postv_nods.txt")
> targets_nod
   SampleNumber                                          FileName    Cy3
Cy5
1             1                        135kt_251485025987_1_4.txt normal
tumor
2             2                        157kt_251485025985_1_3.txt normal
tumor
3             3                        159kt_251485025985_1_4.txt normal
tumor
4             4                        171kt_251485026134_1_3.txt normal
tumor
5             5                        179kt_251485026134_1_4.txt normal
tumor
6             6                         28kt_251485025987_1_1.txt normal
tumor
7             7                         58kt_251485025986_1_1.txt normal
tumor
> RG<-read.maimages(targets_nod$FileName, source="agilent")
> RG<-backgroundCorrect (RG,method="none")
> MA<-normalizeWithinArrays(RG, method="loess")
> MA <- normalizeBetweenArrays(RG, method="quantile")

thank you,
Neeraj Rana
IISC Banglore,INDIA.

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