Dear Gregory, ? Thank you for the answer! ? Now I'm not able to use simpleaffy package for these two chips because I need to create qcdef files for arrays. An error occurred when I try to call qc(): ? Error in setQCEnvironment(cdfn) : ? Could not find array definition file ' u133x3pcdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. ? ? Best regards, Kirill Prusov ? 27.09.2013, 12:20, "gregory voisin" <voisingreg at="" yahoo.fr="">: ? ? Hello,? ? Create your abatch object and use this code. Greg ? ? #Script R ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # #voisin Greg ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # #2013 ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # #R basis ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # #Objectives: ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? ? # #Generate Quality Control for Affymetrix experiment? ################################################################### ######### #### ####load library library(simpleaffy) library(affyPLM) ? ? ? ? ? abatch.qc = qc(abatch) ? avbg(abatch.qc) ? sfs(abatch.qc) ? percent.present(abatch.qc) ? metric_AFF=data.frame(avbg(abatch.qc), sfs(abatch.qc),percent.present(abatch.qc)) ? ? ##Internal Control Grap ? abatch.qc at bioBCalls ? spikeInProbes(abatch.qc) ? concentration <- log(c(1.5, 5, 25, 100)) ? x_values <- array(concentration, c(4, length(abatch))) ? x_values <- t(x_values) ? y_values <- spikeInProbes(abatch.qc) ? ? # plot the values in a scatterplot of y as function of x ? plot(x_values, y_values, col=1:12, main="Spike-in performance", xlab="log (concentration in pM)", ylab="log2(expression)") ? ? ? legend(legend=sampleNames(abatch), x=3.5, y=10, lty=1, col=1:12, cex=0.75) ? ? for (i in 1:length(abatch)){ ? ? y_values <- spikeInProbes(abatch.qc)[i,] ? ? lm_spike <- lm(y_values~concentration) ? ? slope <- coef(lm_spike) [2] ? ? intercept <- coef(lm_spike) [1] ? ? abline(intercept, slope, col=i) ? } ? #RNA degradation graph RNAdeg = AffyRNAdeg(abatch) summaryAffyRNAdeg(RNAdeg) plotAffyRNAdeg(RNAdeg) ? ? ## image plots for raw data, log transform and residuals for the sample 5. image(abatch[,5],transfo =F) image(abatch[,5], transfo=log) ? fit.model <- fitPLM(abatch, model=PM ~ -1 + probes + samples) image(fit.model, which = 5, type = "resids") ? ################################################################### ######### ##### col.for.boxplot = c(rep("blue", 3), rep("red", 3),rep("green", 3),rep("grey", 3)) ? boxplot(abatch, col= col.for.boxplot, main = "Expression level of raw data", ylab = "expression level (raw)") ? eset <- affy_experiment[[3]] boxplot(eset, col= col.for.boxplot, main = "Expression level of rma data", ylab = "expression level (rma)") ? ################################################################### ######### ##### ? ? ? _________________________________________________________________ De? : b a <[1]haba18 at yandex.ru> ?? : Hostname Romeokp <[2]bioconductor at r-project.org> Envoy?? le : Jeudi 26 septembre 2013 10h46 Objet? : [BioC] QC for HT HGU133A and U133A X3P Dear colleagues, I need some QC tests (scale factor, background level, GADPH, beta- actin and other) for these two chips. ht_hgu133a chip is very similar to the hgu133a chip and I can use hgu133acdf.qcdef? file for this analysis (see this: [3]https://stat.ethz.ch/pipermail/bioconductor/2011-October/041603. html). But I need to use another QC method from yaqcaffy package (spike controls for lys, phe, thr, dap) and it's not possible to change any file in yaqc library I think.? For another chip, U133A X3P I've not found any information about QC. I suppose this chip is very similar to hgu133plus2 chip but I'm not sure. And, the question about yaqcaffy package remains open. Is it possible to use simpleaffy and yaqcaffy packages methods for these two chips? Thank you! Kirill Prusov _______________________________________________ Bioconductor mailing list [4]Bioconductor at r-project.org [5]https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: [6]http://news.gmane.org/gmane.science.biology.informatics.conductor References 1. mailto:haba18 at yandex.ru 2. mailto:bioconductor at r-project.org 3. https://stat.ethz.ch/pipermail/bioconductor/2011-October/041603.html 4. mailto:Bioconductor at r-project.org 5. https://stat.ethz.ch/mailman/listinfo/bioconductor 6. http://news.gmane.org/gmane.science.biology.informatics.conductor