hi,
i am going to perform variance stabilization on my data sets then i did like below
> library(affy) > library(vsn) > celFiles < list.celfiles() > affyraw=ReadAffy(filenames = celFiles) > fit = vsn2(affyraw) vsn2: 506944 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. > nkid = predict(fit, newdata=affyraw) > vsnrma(nkid) vsn2: 506944 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’ Calculating Expression ExpressionSet (storageMode: lockedEnvironment) assayData: 22810 features, 8 samples element names: exprs protocolData sampleNames: Col0 24h primed.CEL.CEL Col0 24h unprimed.CEL.CEL ... Col0 8h unprimed.CEL.CEL (8 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: Col0 24h primed.CEL.CEL Col0 24h unprimed.CEL.CEL ... Col0 8h unprimed.CEL.CEL (8 total) varLabels: sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: ath1121501 > a < vsnrma(nkid) vsn2: 506944 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. Calculating Expression > celFiles < list.celfiles() > affyraw=ReadAffy(filenames = celFiles) > eset < justvsn(celFiles) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘vsn2’ for signature ‘"character"’ > justvsn(a) vsn2: 22810 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. ExpressionSet (storageMode: lockedEnvironment) assayData: 22810 features, 8 samples element names: exprs protocolData sampleNames: Col0 24h primed.CEL.CEL Col0 24h unprimed.CEL.CEL ... Col0 8h unprimed.CEL.CEL (8 total) varLabels: ScanDate varMetadata: labelDescription phenoData sampleNames: Col0 24h primed.CEL.CEL Col0 24h unprimed.CEL.CEL ... Col0 8h unprimed.CEL.CEL (8 total) varLabels: sample varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' Annotation: ath1121501 > a <justvsn(a) vsn2: 22810 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. Error in a < justvsn(a) : comparison (3) is possible only for atomic and list types > a < justvsn(a) vsn2: 22810 x 8 matrix (1 stratum). Please use 'meanSdPlot' to verify the fit. 

