# # # R代码从装饰图案的affypdnn来源。Rnw“# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块1号:引文# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #引文(包=“affypdnn”) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块2号:init # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(affypdnn) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块3号:afbatch # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #库(affydata)数据(稀释)afbatch < -稀释# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块数量4:hgu95av2Params # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # (hgu95av2.pdnn.params)参数数据。chiptype < - hgu95av2.pdnn。params # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块5号:energyFiles # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # dir(系统。文件(“exampleData”,包=“affypdnn”)) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块6号:experimentSpecific # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #(“参数数据。稀释”,包= " params < - params affypdnn”)。稀释rm (params.dilution) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块7号:pmLevel # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # ppset.name < - c (“41206 _r_at”、“31620”_at) ppset <——probeset (afbatch ppset.name) # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #代码块8号:pmLevelPlot # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # par (mfrow = c(2, 2))(我在1:2){探针。pdnn < - pmcorrect。pdnnpredict (ppset[[我]],参数,参数个数。chiptype =参数。chiptype) plot(ppset[[i]], main=paste(ppset.name[i], "\n(raw intensities)")) matplotProbesPDNN(probes.pdnn, main = paste(ppset.name[i], "\n(predicted intensities)")) } ################################################### ### code chunk number 9: expressopdnn ################################################### ids <- ls(getCdfInfo(afbatch))[1:10] eset <- expressopdnn(afbatch, bg.correct = FALSE, normalize = FALSE, findparams.param = list(params.chiptype = params.chiptype, give.warnings=FALSE), summary.subset=ids)