[BioC] Could you help me

[James W. MacDonald]

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