[BioC] Could you help me

[Holger Schwender]

The problem is that the specification of cl currently differs between SAM
and EBAM. When performing a SAM analysis you can specify cl in the way that
you have specified it. In an EBAM analysis, this way of specification is
currently not implemented. I hope that I can implement this soon. This
should be available latest in the next Bioconductor release. 

> Liao, Guiping wrote:
> > Dear everyone:
> > 
> > I am employing the Bioconductor Packages such as Siggenes to analyse
> > Microarray Data. My experiment is  the two class paired case, according
> to
> > arguments of siggenes, I set the cl as follows:
> > 
> >>npr4.cl
> > 
> >    V1 V2
> > 1   1  2
> > 2  -1  2
> > 3   1  5
> > 4  -1  5
> > 5   1  1
> > 6  -1  1
> > 7   1  3
> > 8  -1  3
> > 9   1  4
> > 10 -1  4
> 
>  From the help page for find.a0:
> 
>   cl: a vector containing the class labels of the samples. In the
>            two class unpaired case, the label of a sample is either 0
>            (e.g., control group) or 1 (e.g., case group).  In the two
>            class paired case, the labels are the integers between 1 and
>            n/2 (e.g., after treatment group) and between -1 and -n/2
>            (e.g., before treatment group), where n is the length of 'cl'
>            and k is paired with -k. For one group data, the label for
>            each sample should be 1.
> 
> So find.a0 is expecting a vector rather than the matrix you are using. I 
> believe you want something like:
> 
> npr4.cl <- npr4.cl[,1]*npr4.cl[,2]
> 
> You also don't have enough samples to do 26282 permutations, nor (I 
> suspect) do you really want to wait that long. I would suggest something 
> more reasonable like 500 or 1000.
> 
> Jim
> 
> 
> > 
> > I run the find.a0, it gives me a wrong message:unpaired case???  ::
> > 
> >  a0 <-
> > find.a0(npr4,npr4.cl,B=26282,balanced=FALSE,mat.samp=NULL,delta=0.485,
> > + alpha=(0:9)/10,
> > include.0=TRUE,p0=NA,plot.legend=TRUE,na.rm=FALSE,rand=1234567)
> > EBAM Analysis for the two class unpaired case. 
> >  
> > Warning: Expected classlabels are 0 and 1. cl will thus be set to 0 and
> 1. 
> >  
> > Error in "[<-.data.frame"(`*tmp*`, which(cl == min(lev)), value = 0) : 
> >         new columns would leave holes after existing columns
> > 
> > So, I dont know what's wrong? Yet that cl will be set to 0 and 1is for
> the
> > unpaired case. 
> > 
> > I am sure that  you can help me.
> > 
> > Tthanks so much.
> > 
> > Guiping Liao
> > PBI, NRC, Canada
> > 
> > 
> > 	[[alternative HTML version deleted]]
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> 
> -- 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 
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