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 -- Sent via the guest posting facility at bioconductor.org.

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 > > > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]