Dear Biostars community,
I am analyzing a microarray gene expression dataset generated with the Illumina human ht-12 v4 platform. I have loaded the raw image data to Genome Studio and calculated the sample_probe_profile (I am interested in the probe-level measurement). I want to extract the raw data and then use the neqc() function from Bioconductor's limma package for preprocessing. I read at the documentation that, for more accurate results, a file called Control_Probe_Profile is needed. Genome Studio is supposed to extract this under Analysis > Reports > Final Review...However, I cannot see it there. I only see Group and Sample Probe and Gene Profile files (4 in total). Where is the Control_Probe_Profile file located?
Thank you very much for any help!