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hg19 # give the samples descriptive names targets$ID Luminespib supplier annotation: ilmn12.hg19 Quality control Once the data has been imported into R, we can evaluate its quality. Firstly, we need to calculate detection p-values. We can generate a detection p-value for every CpG in every sample, which is indicative of the quality of the signal. The method used by minfi to calculate detection p-values Fleroxacin compares the total signal ( M + U) for each probe to the background signal level, which is estimated from the negative control probes. Very small p-values are indicative of a reliable signal whilst large p-values, for example >0.01, generally indicate a poor quality signal. Plotting the mean detection p-value for each sample allows us to gauge the general quality of the samples in terms of the overall signal reliability ( Figure 2). Samples that have many failed probes will have relatively large mean detection p-values. Figure 2. Mean detection p-values summarise the quality of the signal across all the probes in each sample. # calculate the detection p-values RO4929097 mouse detP