[BioC] affycoretools: group parameter

[James W. MacDonald]

Ingrid H. G. Østensen wrote:
> Hi
> 
> Why is it [-14] and not [-15]? Is the group parameter zero based?

Actually I was completely off. The third replicate of the fourth group 
would be the 12th member of the vector, so you want [-12]. Although any 
of [-10], [-11], [-12] would result in the same thing, as all you want 
to do is end up with a groups vector that looks like

1 1 1 2 2 2 3 3 3 4 4 5 5 5 6 6 6

So removing any of the 4s will give you what you want.

Sorry for the confusion.

Best,

Jim


> 
> Regards,
> Ingrid
> 
> 
> 
> 
>  
> 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
>>
>>
>>
>>
>>[[alternative HTML version deleted]]
>>
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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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