[BioC] affycoretools: group parameter

[James W. MacDonald]

Hi Ingrid,

Ingrid H. G. Østensen wrote:
> Hi
> 
> I have an experiment with 24 cel files divided into 6 groups (4 of
> each type). In affycoretools the group parameter would be like this:
> groups = rep(1:24, each = 4).
> 
> After the QC I found out that one of the arrays was really bad and
> had to be removed. In other words there are now 5 groups with 4
> arrays and one with 3 arrays. What should I put in the group
> parameter now? I have tried different things but nothing has worked
> so far.

The groups argument (not a parameter) you are specifying isn't correct 
to begin with. You want groups = rep(1:6, each = 4). The groups argument 
you are specifying now is a numeric vector of length 96, instead of 
length 24. I should probably put in some error checking to prevent 
mis-specified groups arguments.

Anyway, the groups argument just specifies what group each celfile 
belongs to, so you can simply subset the correct argument to remove one 
of the replicates for the group that has been reduced. For instance, 
let's say you removed the third replicate of the fourth group. You can 
then specify the groups argument like this:

groups = rep(1:6, each=4)[-14]

Best,

Jim



> 
> Regards, Ingrid
> 
> 
> 
> 
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> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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