[BioC] help with estrogen dataset in factdesign package

[Robert Gentleman]

Hi Alberto,


Alberto Goldoni wrote:
> 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.

 You *must* jointly normalize, and that is what we did.
There is no such thing as an exprset anymore (they were deprecated a long time ago).

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

 You seem very confused. pData accesses the phenotypic data. I have no idea
where you are getting 500 genes from? Perhaps you have a script or something?
Perhaps you are reading the vignette? If the vignette then you have access to
all the code and can easily answer these questions.
  I think you will need to be more explicit about where you are getting 500
genes from (but I don't see how it has anything to do with pData(estrogen).)

 best wishes
   Robert

> 
> that all
> best regards
> 
> 

-- 
Robert Gentleman, PhD
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
PO Box 19024
Seattle, Washington 98109-1024
206-667-7700
rgentlem at fhcrc.org