[BioC] list of significant genes (siggenes)

[Holger Schwender]

> --- Ursprüngliche Nachricht ---
> Von: Assa Yeroslaviz <Assa.Yeroslaviz at uni-duesseldorf.de>
> An: "bioconductor at stat.math.ethz.ch" <bioconductor at stat.math.ethz.ch>
> Betreff: [BioC] list of significant genes (siggenes)
> Datum: Fri, 28 Oct 2005 16:39:08 +0200
> 
> Hi,
> 
> i need some helpediting my resluts.
> 
> I have a data frame( matrix ), whereas on the first column are the names
> of my
> items. Then I have a second object. This is the output of the line:
> > list.siggenes(data.out, delta)
> "item_1! "item_2" "item_3" "item_4" ...
> 
> 1. Is this object is a vector or  just a list?

It's a vector containing the names of the significant genes.

> 2. How can i change this object to a matrix?

E.g., matrix(list.siggenes(data.out,delta)). But I don't think that this
actually is what you really want to have.

> 
> my second problem is in comparing both of the data. I want to compare the
> data
> frame with the list from 'list.siggenes' and to cut out all the line,
> which
> don't appear in both objects.

If your data set is called data and (as you have said) the first column of
data contains the gene names, then one way to do this is

R> rownames(data)<-data[,1]
R> data<-data[,-1]  # this step is actually not needed
R> sig.data<-data[list.siggenes(data.out,delta),]

Best,
Holger



> 
> can anyone please help me?
> 
> THX
> 
> Assa
> 
> 
> --
> Assa Yeroslaviz
> Lötzenerstr. 15
> 51373 Leverkusen
> 
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