Many thanks, but now the situation is like this:

> pData(eset.iqr.50)
              sample   ES TYPE
SHR-PUFA5.CEL      1 PUFA  SHR
SHR-PUFA6.CEL      2 PUFA  SHR
SHR-st7.CEL        3 PUFA  SHR
SHR-st8.CEL        4 PUFA  SHR
WK-PUFA3.CEL       5   ST   WK
WK-PUFA4.CEL       6   ST   WK
WK-st1.CEL         7   ST   WK
WK-st2.CEL         8   ST   WK
> head(pData(eset.iqr.50))
              sample   ES TYPE
SHR-PUFA5.CEL      1 PUFA  SHR
SHR-PUFA6.CEL      2 PUFA  SHR
SHR-st7.CEL        3 PUFA  SHR
SHR-st8.CEL        4 PUFA  SHR
WK-PUFA3.CEL       5   ST   WK
WK-PUFA4.CEL       6   ST   WK
> varMetadata(eset.iqr.50)
          labelDescription
sample arbitrary numbering
ES              What ES is
TYPE          What TYPE is

i would like to remove "sample" and leave only ES and TYPE,

can you help me again?

Best regards.





2009/5/27 Martin Morgan <mtmorgan@fhcrc.org>

> Hello Alberto --
>
> Alberto Goldoni <alberto.goldoni1975@gmail.com> writes:
>
> >> Hello to everybody,
> >> i have a little problem with my dataset. Actually my data using
> >> pData(eset.irq.50) is like this:
> >>
> >> > eset.irq.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:
> >>     sample: arbitrary numbering
> >> featureData
> >>   featureNames: 1367555_at, 1367556_s_at, ..., 1399089_at  (1227 total)
> >>   fvarLabels and fvarMetadata description: none
> >> experimentData: use 'experimentData(object)'
> >> Annotation: rat2302
> >>
> >>
> >> > pData(eset.irq.50)
> >>                                        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
> >>
> >> i would like to modify these data in order to obtain:
> >>
> >> > pData(eset.irq.50)
> >>                                 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
>
> do you mean like
>
> > dim(sample.ExpressionSet)
> Features  Samples
>     500       26
> > head(pData(sample.ExpressionSet))
>     sex    type score
> A Female Control  0.75
> B   Male    Case  0.40
> C   Male Control  0.73
> D   Male    Case  0.42
> E Female    Case  0.93
> F   Male Control  0.22
> > sample.ExpressionSet[["ES", labelDescription="What ES is"]] <-
> +     factor(c("PUFA", "ST"))
> > sample.ExpressionSet[["TYPE", labelDescription="What TYPE is"]] <-
> +     factor(rep(c("SHR", "WK"), each=13))
> > head(pData(sample.ExpressionSet))
>     sex    type score   ES TYPE
> A Female Control  0.75 PUFA  SHR
> B   Male    Case  0.40   ST  SHR
> C   Male Control  0.73 PUFA  SHR
> D   Male    Case  0.42   ST  SHR
> E Female    Case  0.93 PUFA  SHR
> F   Male Control  0.22   ST  SHR
> > varMetadata(sample.ExpressionSet)
>      labelDescription
> sex        Female/Male
> type      Case/Control
> score    Testing Score
> ES          What ES is
> TYPE      What TYPE is
>
> ?
>
> Hope that helps,
>
> Martin
>
> >> in order to gave to me the possibility to perform factDesign analysis.
> >>
> >> Somebody can help me?
> >>
> >>
> >> BEST REGARDS.
> >>
> >>
> >>
> >> --
> >> -----------------------------------------------------
> >> Dr. Alberto Goldoni
> >> Bologna, Italy
> >> -----------------------------------------------------
> >>
>
> --
> Martin Morgan
> Computational Biology / Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N.
> PO Box 19024 Seattle, WA 98109
>
> Location: Arnold Building M1 B861
> Phone: (206) 667-2793
>



-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Bologna, Italy
-----------------------------------------------------

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