[BioC] Affycoretools - Limit genes in Venn diagram by fold change?

[Quentin Anstee]

Hi Jim,

Thanks again!

Quentin 

> -----Original Message-----
> From: James W. MacDonald [mailto:jmacdon at med.umich.edu] 
> Sent: 03 March 2006 17:56
> Cc: Quentin Anstee; 'Bioconductor'
> Subject: Re: [BioC] Affycoretools - Limit genes in Venn 
> diagram by fold change?
> 
> James W. MacDonald wrote:
> > Hi Quentin,
> > 
> > Quentin Anstee wrote:
> > 
> >>Dear List,
> >> 
> >>Having processed my affy data and fitted a linear model 
> with limma, I 
> >>would like to export a Venn diagram to illustrate the 
> number of genes 
> >>in each of my 3 comparisons. I have used the following script which 
> >>outputs all the genes that are significantly differentially 
> expressed 
> >>and is based on the affycoretools package:
> >> 
> >>rslt<-decideTests(fit2, adjust.method="fdr")
> >>vc<-vennCounts2(rslt,method="both")
> >>vennDiagram(vc,cex=0.8)
> >>vennSelect(mySubSet,fit2,design,rslt,method="both")
> >>
> >>What I would like to do is to reduce the number of genes that are 
> >>counted in the Venn diagram so that only those with a 1.5 fold 
> >>increase or decrease in expression are included.
> >> 
> >>Please could you advise me how this can be achieved?
> > 
> > 
> > I would think something like:
> > 
> > idx <- abs(fit2$coefficients) > 1.5
> 
> Hmmm. Make that
> 
> idx <- abs(fit2$coefficients) > log2(1.5)
> 
> unless you really want a log difference of 1.5 rather than a 
> 1.5 fold change.
> 
> Jim
> 
> 
> 
> 
> > rslt <- rslt * idx
> > vennSelect(mySubSet, fit2, design, rslt, method = "both")
> > 
> > would do it.
> > 
> > HTH,
> > 
> > Jim
> > 
> > 
> > 
> >> 
> >>Very many thanks,
> >>
> >>Quentin
> >>
> >>	[[alternative HTML version deleted]]
> >>
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> > 
> > 
> > 
> 
> 
> --
> James W. MacDonald, M.S.
> Biostatistician
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
>