I have a data set containing 2956 genes and normalized their expression values(the experiment is conducted by using affymetrix array).these expression values are the usual summary value calculated for affymetrix array.that means I have only one expression value for one gene and their associated P-value that indicates is there that particular gene is differentially expressed in that sample. and these 2956 genes expression level are given for 39 conditions. How can i detect the number of Important genes?
Your questions is not very clear but from what I understand "important genes" are typically with a P-value <= 0.05 and a fold-change between conditions >= 2. These values are rather popular but adjust them according to your experiments. You also have to consider normalization first but you have to tell us more about your project
Well Pasta, let me clear my problem. My data set is like as follows:
gene_1 6.2 0.73717
gene_2 31.9 0.51489
By this way 2956 gene's info is given for all the 39 conditions. Say here i have just given one condition's example.same set up is given for all the remaining 38 conditions.