[BioC] EdgeR- equal number of columns per group?

[Lana Schaffer]

Davis,
Thanks.  I was able to fix my problem.
Lana

-----Original Message-----
From: Davis McCarthy [mailto:dmccarthy at wehi.EDU.AU] 
Sent: Monday, May 23, 2011 3:42 PM
To: Lana Schaffer
Cc: 'bioconductor at r-project.org'
Subject: Re: [BioC] EdgeR- equal number of columns per group?

Hi Lana

It certainly should be possible for you to use all of your information. 

What is the output from dim(D)? 

Somehow there is a mismatch between the number of columns of your object D and the group labels you are assigning. The group vector you define, c(rep("d45HVC",2),"d45WB"), should indeed be of length 3, so it seems that D does not consist of exactly three columns.

Cheers
Davis


On May 24, 2011, at 5:21 AM, Lana Schaffer wrote:

> Hi,
> I got this message when trying to use 2 columns for HVC and 1 column for WB.
> 
>> d <- DGEList(counts = D, group = c(rep("d45HVC",2),"d45WB"))
> Error in DGEList(counts = D, group = c(rep("d45HVC", 2), "d45WB")) :
>  Length of 'group' must equal number of columns in 'counts'
> 
> So there is no way for me to use all my information (columns) ?
> 
> 
> Lana Schaffer
> Biostatistics, Informatics
> DNA Array Core Facility
> 858-784-2263
> 
> 
> 	[[alternative HTML version deleted]]
> 
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------------------------------------------------------------------------
Davis J McCarthy
Research Technician
Bioinformatics Division
Walter and Eliza Hall Institute of Medical Research
1G Royal Parade, Parkville, Vic 3052, Australia
dmccarthy at wehi.edu.au
http://www.wehi.edu.au




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