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