Hi Saroj, Thanks for your suggestions. Abhilash On Thu, Jun 11, 2009 at 8:19 PM, Saroj K Mohapatra <saroj@vt.edu> wrote: > Hello Abhilash: > >> ... where we have 5 normal samples (untreated) >> with 6 patients treated with drug A and 5 patients treated with drug A + >> B. The biologists question is there any serious perturbations of the >> genes >> between two groups (Treated with A only and treated with A+B). >> > I agree with your choice: by applying a p.value/ratio threshold in limma > one can find the genes affected by drug A (A-Control) and genes affected by > drug A+B (AB-Control). Union of the two sets would have all the genes > differentially expressed (d.e.) by EITHER treatment; intersection would have > the genes d.e. in BOTH. > >> They are >> interested to represent the same by a cluster. >> >> > Do you mean a heatmap from hierarchical clustering? You could select the > genes and then get the expression matrix for all three groups of samples, > order them by genes only (not samples) and the resulting heatmap would have, > hopefully, regions of gene expression showing difference between control and > treatments. > > Best, > > Saroj > >> I am just wondering, whether I should do separate analysis of those two >> groups using limma and cluster together by selecting genes using some >> parameters such as P value or fold value.? >> or >> Whether I should do analysis together using limma and cluster it by >> selecting genes by fold value of P value.? >> >> It will be of great help if any one of you could provide suggestions on >> the >> same. >> >> Thanks in advance. >> >> Regards, >> Abhilash >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >> >> > > -- Regards, Abhilash [[alternative HTML version deleted]]