[BioC] Problem in analysing Agilent single color data using LIMMA

[James W. MacDonald]

On 4/27/2012 1:48 AM, Muralidharan V wrote:
> Hai,
>
> I had few questions regarding the analysis of  Agilent microarray data
> using the LIMMA pacakge.
>
>   Is it possible to analyse the single color data using the R+Bioconductor
> using the LIMMA package? We dont have the replicates instead of that we
> have pooled the samples before sending for the analysis.
> So is it possible to use the LIMMA package without having any replicates.

You can analyze single color Agilent microarray data with limma. 
However, if you don't have replicates you cannot do anything more than 
compute fold change (which being trivial, is not something that limma does).

Best,

Jim


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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099