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

[James W. MacDonald]

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]]
>>
>>_______________________________________________
>>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