Hello to everybody

i'm writing this email because i need some explanation about the "estrogen"
dataset analyzed in the "factDesign" package.
I have to perform the same analysis on 8 sample (affychip):

> pData(data.rma)

>
>   ES              TYPE
> SHR-PUFA5.CEL     PUFA          SHR
> SHR-PUFA6.CEL     PUFA          SHR
> SHR-st7.CEL           ST               SHR
> SHR-st8.CEL           ST               SHR
> WK-PUFA3.CEL      PUFA           WK
> WK-PUFA4.CEL      PUFA           WK
> WK-st1.CEL            ST                WK
> WK-st2.CEL            ST                WK
>


> 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


What i need to know is if i have to analyze all toghether: nomalization with
rma, filtering with IQR and then i can perform factDesign technique or i
have to threat the two group (1:4) and (5:8) separately and then to rebuild
and exprset at the end.

So my curiosity is to understand how the "estrogen" dataset has been
analyzed in order to obtain the 500 genes listed in pData(estrogen).

that all
best regards


-- 
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Dr. Alberto Goldoni
Bologna, Italy
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