[BioC] Affycoretools - Limit genes in Venn diagram by fold change?
James W. MacDonald
jmacdon at med.umich.edu
Fri Mar 3 18:55:51 CET 2006
James W. MacDonald wrote:
> Hi Quentin,
> Quentin Anstee wrote:
>>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
>>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
> rslt <- rslt * idx
> vennSelect(mySubSet, fit2, design, rslt, method = "both")
> would do it.
>>Very many thanks,
>> [[alternative HTML version deleted]]
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James W. MacDonald, M.S.
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
Ann Arbor MI 48109
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