Hi list! After reading in may data, which is an affybatch object HG-U133A with 20 samples (2 groups with 10 samples), I have no problems in visualizing my data (e.g. with boxplots, MAplots,...). After normalizing my data sets with gcrma I now have an exprSet object and I don?t have a clue in which ways I can visualize the exprSet. Or is there a possibility to normalize my data without changing it into an exprSet? I haven?t found proper information on the i-net that is why I have to bug you, but a link with good examples would be great too! thank you very much in advance! sincere, igor

I do not understand this at all. An AffyBatch object si basically an exprSet with a few other slots containing annotation information and nrow/ncol. So every method you have for visualizing the AffyBatch object should basically carry over... depending on _how_ you do it. Kasper On Nov 9, 2005, at 2:02 PM, Igor Androv wrote: > Hi list! > > After reading in may data, which is an affybatch object HG-U133A > with 20 > samples (2 groups with 10 samples), I have no problems in > visualizing my > data (e.g. with boxplots, MAplots,...). After normalizing my data > sets with > gcrma I now have an exprSet object and I don?t have a clue in which > ways I > can visualize the exprSet. Or is there a possibility to normalize > my data > without changing it into an exprSet? > > I haven?t found proper information on the i-net that is why I have > to bug > you, but a link with good examples would be great too! > > thank you very much in advance! > > sincere, > igor > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor

AffyBatch extends exprset, and the R docs describe the structure of both. These objects allow you to keep together the expression data as well as phenotype data, etc., in one object. For further visualization/analysis of your data, you can access the expression values in the exprset with the exprs function (which is simply an accessor function for the exprs slot of the object), as in: mydata <- exprs(myExprSet) mydata would then be a matrix containing the normalized summary gene expression values produced by gcrma for each case/chip, which you could plot, etc. -Eric >Subject: [BioC] AffyBatch <-> exprSet > >Hi list! > >After reading in may data, which is an affybatch object HG-U133A with 20 >samples (2 groups with 10 samples), I have no problems in visualizing my >data (e.g. with boxplots, MAplots,...). After normalizing my data sets with >gcrma I now have an exprSet object and I don?t have a clue in which ways I >can visualize the exprSet. Or is there a possibility to normalize my data >without changing it into an exprSet? > >I haven?t found proper information on the i-net that is why I have to bug >you, but a link with good examples would be great too! > >thank you very much in advance! > >sincere, >igor _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor This email message, including any attachments, is for the so...{{dropped}}