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

[Ekta Jain]

Hi Jim,
I am using an affymetrix chip data. I need to analyse my dataset for differential gene expression (LIMMA). Each gene can be referenced by multiple probesets and while performing LIMMA the expression values of these multiple probesets gets averaged and this averaged value is assigned to that gene. I need to be able to simply select the probeset with the highest expression value to represent a gene. 

LIMMA by default averages the probeset values.

I am not sure if i need to modify any default settings in LIMMA or use another package.

Thanks

Regards,
Ekta

-----Original Message-----
From: James W. MacDonald [mailto:jmacdon at uw.edu] 
Sent: 22 February 2012 19:26
To: Ekta [guest]
Cc: bioconductor at r-project.org; Ekta Jain
Subject: Re: [BioC] Use probesets with highest baseline expression for differntial gene expression in LIMMA

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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