[BioC] Use probesets with highest baseline expression for differntial gene
Ekta Jain
Ekta_Jain at jubilantbiosys.com
Thu Mar 1 05:40:57 CET 2012
Dear Gordon,
That worked fantastic.
Thank you very much.
Best Regards,
Ekta
-----Original Message-----
From: Gordon K Smyth [mailto:smyth at wehi.EDU.AU]
Sent: 24 February 2012 05:00
To: Ekta Jain
Cc: Bioconductor mailing list
Subject: Use probesets with highest baseline expression for differntial gene
Dear Ekta,
Jim as already pointed out that you have some incorrect perceptions about
what limma does by default.
If you need to keep one probe for each gene symbol after a limma lmFit,
and you want to choose the probe with highest average expression, it is
easy to do like this. I will assume that your linear model fit object is
called 'fit', and your annotation includes a column called "Symbol"
containing the gene symbol.
o <- order(fit$Amean, decreasing=TRUE)
dup <- duplicated(fit$genes$Symbol[o])
fit.unique <- fit[o,][!dup,]
Now your fit object fit.unique has only one row for each symbol.
This sort of filtering has been done in many papers when it is wished to
match symbols across platforms, or to do gene set testing.
Best wishes
Gordon
------------------ original message ----------------
[BioC] Use probesets with highest baseline expression for differntial
gene expression in LIMMA
Ekta Jain Ekta_Jain at jubilantbiosys.com
Thu Feb 23 04:06:09 CET 2012
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
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