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

[James W. MacDonald]

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
rslt <- rslt * idx
vennSelect(mySubSet, fit2, design, rslt, method = "both")

would do it.

HTH,

Jim


>  
> Very many thanks,
> 
> Quentin
> 
> 	[[alternative HTML version deleted]]
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor


-- 
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