Dear Gordon, That worked fantastic. Thank you very much. Best Regards, Ekta -----Original Message----- From: Gordon K Smyth [mailto:smyth@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@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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:22}}