Dear All, I have problems in labeling the heatdiagram of limma package. My layout consistes of following: layout=list(ngrid.r=12,ngrid.c=4,nspot.r=16,nspot.c=17) There are 13056 spots on the slide. I have done analysis by limma package but finally when i want to plot heatdiagram, all clones which are differenetially expressed are labeled on Y axis (which makes it impossible to read the label), where as i am interested in looking at only top 100 genes on the heatdiagram. Please let me know where do I specify this top 30 command. I have followed example dataset(weaver experiment :2* 2 factorial design) Thanks in advance Binita ============================== Binita Dutta, PhD MicroArray Facility(MAF) UZ Gasthuisberg Onderwijs en Navorsing Herestraat 49 3000 Leuven Belgium

Hi Binita, On Mon, 14 Jun 2004, Binita Dutta wrote: > I have done analysis by limma package but finally when i want to plot > heatdiagram, all clones which are differenetially expressed are labeled on > Y axis (which makes it impossible to read the label), where as i am I'm not so familiar with the new heatDiagram function in limma, but in the old heatdiagram function (lower case 'd') (still available in limma), you can specify critical.primary and critical.other. Choosing higher values for these will limit the number of genes displayed in your heatdiagram. Have a look at the help for heatdiagram: ?heatdiagram The first argument to heatdiagram could be your matrix of (moderated) t statistics (i.e. fit$t, after running eBayes on fit). Then critical.primary and critical.other would be (moderated) t statistic values. Remember that the heatdiagram is plotted relative to one "primary" contrast. For this contrast the colors should appear in order from green to red (or the other way around, depending on how you look at the diagram). This should help you to understand the difference between the two t statistic threshold values: critical.primary and critical.other. So for example, you could try increasing critical.primary from the default value of 4 to 10 and increase critical.other from 3 to 8. To get an idea of how much to increase them in your case, have a look at the "t" column in your toptable. Hope this helps, James