Hello, is there somebody that can help me with filtering function? After the normalization of all my dataset toghether, i obtain "data.rma" like this: > pData(data.rma) sample SHR-PUFA5.CEL 1 SHR-PUFA6.CEL 2 SHR-st7.CEL 3 SHR-st8.CEL 4 WK-PUFA3.CEL 5 WK-PUFA4.CEL 6 WK-st1.CEL 7 WK-st2.CEL 8 > data.rma ExpressionSet (storageMode: lockedEnvironment) assayData: 31099 features, 8 samples element names: exprs phenoData sampleNames: SHR-PUFA5.CEL, SHR-PUFA6.CEL, ..., WK-st2.CEL (8 total) varLabels and varMetadata description: sample: arbitrary numbering featureData featureNames: 1367452_at, 1367453_at, ..., AFFX-TrpnX-M_at (31099 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: rat2302 i would like to filter with the IQR only the [1,2 samples VS 3,4] and the [5,6 VS 7,8] and to add the two results in order to obtain this: > eset.iqr.50 ExpressionSet (storageMode: lockedEnvironment) assayData: 1227 features, 8 samples element names: exprs phenoData sampleNames: SHR-PUFA5.CEL, SHR-PUFA6.CEL, ..., WK-st2.CEL (8 total) varLabels and varMetadata description: TYPE: WK=RATTO NORMALE o SHR=RATTO IPERTESO DIETA: Con PUFA=OMEGA3 o ST=ALIMENTAZIONE STANDARD featureData featureNames: 1367555_at, 1367556_s_at, ..., 1399089_at (1227 total) fvarLabels and fvarMetadata description: none experimentData: use 'experimentData(object)' Annotation: rat2302 usually i use this script: iqr <- function(x)(IQR(x)>0.5) ff <- filterfun(iqr) which <- genefilter(data.rma, ff) sum(which) [1] 1227 eset.iqr.50 <- data.rma[which,] but this is right only for filtering all the samples toghether... best regards -- ----------------------------------------------------- Dr. Alberto Goldoni Bologna, Italy ----------------------------------------------------- [[alternative HTML version deleted]]