The problem is that the specification of cl currently differs between
and EBAM. When performing a SAM analysis you can specify cl in the way
you have specified it. In an EBAM analysis, this way of specification
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
> > Microarray Data. My experiment is the two class paired case,
> > arguments of siggenes, I set the cl as follows:
> > 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
> (e.g., control group) or 1 (e.g., case group). In the
> class paired case, the labels are the integers between 1
> n/2 (e.g., after treatment group) and between -1 and -n/2
> (e.g., before treatment group), where n is the length of
> and k is paired with -k. For one group data, the label
> each sample should be 1.
> So find.a0 is expecting a vector rather than the matrix you are
> 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
> more reasonable like 500 or 1000.
> > I run the find.a0, it gives me a wrong message:unpaired case???
> > a0 <-
> > + 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
> > Error in "[<-.data.frame"(`*tmp*`, which(cl == min(lev)), value =
> > 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
> > 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@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
> Bioconductor mailing list
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