I have started to work with an Illumina dataset [platform:-GPL10558-Illumina HumanHT-12 V4.0 expression beadchip]. I don't have any prior knowledge of Illumina data analysis. I imported my file to R-studio using lumiR function of the Lumi package but the data has some sample replicate and Detection P-value.
Can anyone suggest how I remove these replicate samples and analyze the Illumina data with P-values in it? Do I need to remove the detection P-value or use them in the analysis?