[BioC] Use probesets with highest baseline expression for differntial gene expression in LIMMA

[James W. MacDonald]

Hi Ekta,

On 2/21/2012 10:57 PM, Ekta [guest] wrote:
> Hello All,
> I am relatively new to R and bioconductor. I would like to know if there is a way to alter LIMMA defualt options such that the package instead of averaging signal intensities of probesets selects the probesets with highest baseline
> expression/signal intensity?

You will have to be more precise than that. What exactly do you mean by 
'selects the probesets with highest baseline expression'? Do you just 
want any probesets where one or more samples has high expression? That 
doesn't require limma. Or do you want probesets where some of the 
samples have much higher expression than others?

Best,

Jim


>
> Any help would be greatly appreciated.
>
>
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.9.1 (2009-06-26)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_India.1252;LC_CTYPE=English_India.1252;LC_MONETARY=English_India.1252;LC_NUMERIC=C;LC_TIME=English_India.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] limma_2.18.3
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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