cbil.upenn.edu:RAD.Protocol:3386-3100:Protocol - cbil.upenn.edu:RAD.Protocol:3386-3100:Protocol

gcRMA adjusts for background intensities in Affymetrix array data which include optical noise and non-specific binding (NSB). The main function converts background adjusted probe intensities to expression measures using the same normalization and summarization methods as RMA (Robust Multiarray Average). gcRMA uses probe sequence information to estimate probe affinity to NSB. The sequence information is summarized in a more complex way than the simple GC content. Instead, the base types at each position along the probe determine the affinity of each probe. The background adjusted intensity is computed as the posterior mean of specific binding given the observed intensities and the probe sequences. The background adjusted data are then converted to expression measures with function rma with the option background=FALSE to avoid another round of background correction.
R version, bgversion, fast, gcrma version, normalize, optical.correct, quantile_normalization_context, rho, type
gcRMA quantification (bioconductor)
Experiment E-CBIL-48