At 10:23 PM 28/10/2003, Jason Skelton wrote: >Gordon Smyth wrote: >>Venn diagrams are by their nature simply overall counts. But you can >>easily identify the relevant genes from the 'classification' object from >>which the Venn diagram is computed. > >Not sure how this is done, the object I have created in ClassifyTests has >classification (0 and 1's) and Fstats associated with it >am I looking in the wrong place ? I have a list of genes made from >uniquegenelist is this the list I'm wanting to access ? >My VennCounts object is: > > DIF1 DIF2 DIF3 Counts >[1,] 0 0 0 1925 >[2,] 0 0 1 18 >[3,] 0 1 0 26 >[4,] 0 1 1 5 >[5,] 1 0 0 70 >[6,] 1 0 1 13 >[7,] 1 1 0 90 >[8,] 1 1 1 59 >attr(,"class") >[1] "VennCounts" > >could you give an example of how to associate each of the 8 counts with >genes from the uniquegenelist (OR other) Go one step back, to the classification matrix which comes out of classifyTests(). That gives you a classification matrix with one row for each gene in the uniquegenelist. >>2) >>I'd also like to be able to use the false discovery rate option that can >>beused in classifyTestsP method for my venn diagram but I also want to >>use data that I've received from makeContrasts and contrast.fit which I >>can only use in classifyTests but I can't use "fdr" in that function.... >> >>Is there a particular reason why I can't do this ? > >Yes there is. classifyTests() uses a method intended to control false >discovery rate across contrasts. This is not compatible with the simple >p.adjust() approach to controling FDR across genes. I suggest that you >simply find what unadjusted p-value corresponds to your desired FDR level >and enter that to classifyTests(). > >OK that makes more sense now thanks. > >I have yet more questions about the heatdiagram option >My gene names are very long 28+ characters long is there a heatdiagram >specific command that alters the size of the box that the heatmap covers ? >So that genes appearing on the plot are not truncated (I've tried some of >the R commands for Margins etc but they don't want to work with high level >plots) No there isn't. imageplot truncates names to 15 characters. You would have to modify the code yourself to change that. >Also in the heatdiagram you can specify EB$t and fit$coef >e.g. heatdiagram(newDIF123SEPcontrastfitEB$t, >newDIF123SEPcontrastsfit$coef etc) >you can specify the critical.primary argument which is the critical >value "above" which genes are considered significant. > >BUT > >If you want to use EB$p.value fit$coef >e.g. heatdiagram(newDIF123SEPcontrastfitEB$p.value, >newDIF123SEPcontrastsfit$coef etc) >you can't specify the critical.primary because you need to specify a >maximum value e.g(0.05) rather than minimum as your cutoff Use heatDiagram() instead. That function will accept a classification matrix from classifyTestsP which will allow you to specify your desired p-value cutoff. Gordon >Thanks for you help > >Jason