How to Filter Significant Genes??

[thickrick99]

Hi Everyone,

I am using cummeRbund to do some DE analysis and have 3 samples each having 5 biological replicates. Right now, the number of significant genes in the CuffGeneSet object is 548 with an alpha level of 0.01. I need to plot a heat map for the analysis and I am wondering how to further filter the CuffGeneSet object.

Is there a way to get the top 50 differentially expressed genes for the CuffGeneSet and if so, how can I do this in cummeRbund? I couldn't find any function that would work well in the cummeRbund manual and wasn't sure the best way to filter it down to something more manageable for the heatmap.

Thank you!

[thickrick99]

I am still trying to figure this out however, I don't know how to index the CuffGeneSet object. If there is now solution to my above question, then I guess my only option is to have multiple heat maps (there would be a lot I assume) representing all 548 genes but I don't know how to index the CuffGeneSet in order to do this.