[BioC] Pairwise Comparison error

[James W. MacDonald]

Hi Lakshmi,

First off, you really need to give people more information than this. 
For instance, what package is pairwise.comparison() in? There are over 
350 BioC packages now, so you have to explicitly say what package you 
are using (people aren't generally going to go to great effort to figure 
out where this function comes from, just so they can help you). In 
addition, always give the output of sessionInfo().

On 11/23/2010 2:27 PM, Lakshmi Kastury wrote:
>
> Hi-
> I am in the process of analyzing affymetrix data for prostate cancer patients. I have generated expression data with the RMA function and need to do a pairwise comparison. Can someone please help as to what this error means:
>
> results<- pairwise.comparison(x.rma, "Phenotype", c("normal", "cancerous"), raw.data)
>
> Error in fastT(cbind(a.samples, b.samples), 1:ai, (ai + 1):(ai + bi),  :
>    wrong sets of columns

This indicates that there is some problem with either the column name 
you specified or the column values. Or maybe with the code. It's hard to 
say.

I would first ensure that there is a column name "Phenotype" in the 
pData slot of x.rma, and that there are values "normal","cancerous" in 
that column. If true, there may be a bug.

If there is a bug, the best idea is for you to take things into your own 
hands and see what is happening. So try

library(simpleaffy)
debug(get.fold.change.and.t.test)
results<- pairwise.comparison(x.rma, "Phenotype", c("normal", 
"cancerous"), raw.data)

then when you enter get.fold.change.and.t.test(), step through and make 
sure that you are getting reasonable subsets of your data (e.g., 
a.samples and b.samples look reasonable).

Best,

Jim


>
>
> Thanks!
>   		 	   		
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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