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
-----------------------------------------------------

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