Dear bioconductor forum,
I need help with getting the data I want from agilent microarrays from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=+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 ocurring genes. 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. The problem is that the respective positive and negative ControlTypes to the respective genes are nothing but Agilent control probes on the microarray, the "real" genes I want to destinguish/use aren't marked as positive or negative.
Now my questions: Am I on the right way using the averaged UPC-values? Although the genes I want to use aren't marked as positive or negative ControlTypes, is there still a way to figure out a present/absent pattern for them?
I hope my questions are clearer this time.