[BioC] Thanks

[Fátima Núñez]

Thanx a lot for your prompt answer

Fátima

_______
 

 
Fátima Núñez, PhD
Centre for Cancer Research (CIC)
University of Salamanca-CSIC
Campus Unamuno
37007 Salamanca                                                   
Spain
Phone: + 34 923 294802
Fax:     + 34 923 294743
E-mail: fnunez at usal.es

> -----Original Message-----
> From: Ramon Diaz-Uriarte [mailto:rdiaz at cnio.es]
> Sent: 02 July 2003 13:50
> To: Fátima Núñez; bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] Help with "Error in Summary.factor(..., na.rm =
na.rm)
> : "max" not meaningful for factors", please?
> 
> Hola Fátima,
> 
> I think the problem is that your class labels (rmadata2$Genotype) are
a
> factor, but they should be a vector of integers starting at 0.
> 
> The help for mt.maxT says:
>  "classlabel: A vector of integers corresponding to observation
(column)
>           class labels. For k classes, the labels must be integers
>           between 0 and k-1."
> 
> You can easily achieve that by doing:
> my.classlabels <- as.numeric(rmadata2$Genotype) - 1
> 
> Best,
> 
> Ramón
> 
> 
> 
> On Wednesday 02 July 2003 13:27, Fátima Núñez wrote:
> > Hello all,
> >
> > At the moment I'm trying to obtain adjusted p-values using the maxT
and
> > minP functions on my data as described below, but when I try to
> > implement any of the two I obtain the error shown. I have looked the
> > ?Summary.factor help but I have to admit I didn't quite understand
it.
> > Could anybody please help me with this error in order to know what
I'm
> > doing wrong?
> >
> > >rmadata2$Genotype
> >
> > [1] CONT CONT CONT VAV2 VAV2 VAV2
> > Levels: CONT VAV2
> >
> > > Index1 <- which(rmadata2$Genotype=="CONT")
> > > Index2 <- which(rmadata2$Genotype=="VAV2")
> > > scores <- esApply (rmadata2, 1, function(x) {
> >
> > +       tmp <-t.test(x[Index2], x[Index1], var.equal =TRUE)
> > +       c(mean(tmp$estimate), -diff(tmp$estimate), tmp$statistic,
> > tmp$p.value)
> > +  })
> >
> > > scores <- t(scores)
> > > colnames(scores) <- c("a", "m", "t.test", "p.value")
> > > sum(scores[, 4] <= 0.05)
> >
> > [1] 1130
> >
> > > sum(scores[, 4] <= 0.01)
> >
> > [1] 318
> >
> > > tmp <- mt.rawp2adjp(scores[,4])
> > > adj.p.values <- tmp$adjp[order(tmp$index), -1]
> > > scores <- cbind(scores, adj.p.values)
> > > tmp <- mt.maxT(exprs(rmadata2), rmadata2$Genotype)
> >
> > Error in Summary.factor(..., na.rm = na.rm) :
> >         "max" not meaningful for factors
> >
> > Thanks in advance for your help and sorry if this is not a relevant
> > question for BioC,
> > Fatima
> >
> > _______
> >
> >
> >
> > Fátima Núñez, PhD
> > Centre for Cancer Research (CIC)
> > University of Salamanca-CSIC
> > Campus Unamuno
> > 37007 Salamanca
> > Spain
> > Phone: + 34 923 294802
> > Fax:     + 34 923 294743
> > E-mail: fnunez at usal.es
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
> 
> --
> Ramón Díaz-Uriarte
> Bioinformatics Unit
> Centro Nacional de Investigaciones Oncológicas (CNIO)
> (Spanish National Cancer Center)
> Melchor Fernández Almagro, 3
> 28029 Madrid (Spain)
> Fax: +-34-91-224-6972
> Phone: +-34-91-224-6900
> 
> http://bioinfo.cnio.es/~rdiaz
>