On Wed, Jun 27, 2012 at 5:54 AM, Thileepan [guest]
<guest@bioconductor.org>wrote:

>
> Hi,
>
>  I have a dataset GSE37859 which consist of 3 groups namely
> "NSC","iNSC","MEF".Now I have to create phenodata for the same. I created a
> separate txt file describing group of each samples. Now I wanted to create
> pData for my raw data. Can anyone help me?
>
>  -- output of sessionInfo():
>
> > phenodata #phenodata created in a text file and read inR
>          V1    V2
> 1  GSM929093 iNSC1
> 2  GSM929094 iNSC1
> 3  GSM929095 iNSC1
> 4  GSM929096 iNSC2
> 5  GSM929097 iNSC2
> 6  GSM929098 iNSC2
> 7  GSM929099   NSC
> 8  GSM929100   NSC
> 9  GSM929101   NSC
> 10 GSM929102   MEF
> 11 GSM929103   MEF
> 12 GSM929104   MEF
>
> #This what I get when I give pData(data.raw)
> > pData(data.raw)
>                              sample
> GSM929093_01.iNSC1.1.CEL.gz        1
> GSM929094_02.iNSC1.2.CEL.gz        2
> GSM929095_03.iNSC1.3.CEL.gz        3
> GSM929096_04.iNSC2.1.CEL.gz        4
> GSM929097_05.iNSC2.2.CEL.gz        5
> GSM929098_06.iNSC2.3.CEL.gz        6
> GSM929099_07.WT.NSC.1.CEL.gz       7
> GSM929100_08.WT.NSC.2.CEL.gz       8
> GSM929101_09.WT.NSC.3.CEL.gz       9
> GSM929102_10.WT.MEFs.1.CEL.gz     10
> GSM929103_11.WT.MEFs.3.CEL.gz     11
> GSM929104_12.WT.MEFs.5.CEL.gz     12
>

if this accurately reflects contents of your session, then

pData(data.raw)$group = phenodata$V2

is one way of updating the data.raw ExpressionSet to include the group
information in a
variable called 'group'.  Be sure
to check that the rows are properly ordered in the two objects referred to
in the assignment


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