Question about Agilent microarray data measurement

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7.5 years ago

TS ▴ 30

Dear biostars forum,

I need help with getting the data I want from agilent microarrays from GEO database GSE59408. I used the Bioconductor package "limma" to read in the data from the single-color Agilent microarrays and then the package SCAN.UPC to get the UPC values of the data. I adjusted the variable convThreshold in the function UPC_Generics to 0,1 so the function didn't give me any warning messages. After that I computed the average UPC-value for each of the genes (ProbeNames). My goal is to determine which of the genes in the dataset are present/absent and I already got the hint that I have to think of a own measurement. Am I on the right way using the averaged UPC-values? I am looking for someone who can give me a hint in the right direction because I searched for such a measurement but couldn't find anything.

Thanks in advance, Thomas

agilent microarray limma SCAN.UPC • 1.5k views

ADD COMMENT • link 7.5 years ago by TS ▴ 30

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Dear bioconductor forum,

Wrong forum but we will help :)

ADD REPLY • link 7.5 years ago by GenoMax 141k

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No I think @genomax2 is right with the first part (wrong forum). You'll probably get better advice at the bioconductor forum. Many bioconductors respond only on the bioconductor site and not here.