ib, Look at the status column. I suspect that for this example you given the status is HiData. Cuffdiff considers the expression are very high and no statistic testing would have been done for the gene. fpkm 2=0 could be misleading, as it may not be actually 0. I have encountered in a data set where several genes are expected to be highly expressed in all samples, but one of the fpkm values were all given as 0. Hope this helps. Haiping ---------------------------------------------- JHMI Deep Sequencing and Microarray Core Facility at BRB - Your source for quality service on Microarray studies, NextGen Sequencing, and Data Analysis. http://www.microarray.jhmi.edu/ ---------------------------------------------- Haiping Hao Ph.D. Associate Director Johns Hopkins University Deep Sequencing and Microarray Core Edward D. Miller Research Building 733 N. Broadway, Rm 359 Baltimore, MD 21205 hhao@jhmi.edu Phone: 443-287-9056 Fax: 410-502-6666 On 10/15/2012 5:36 PM, i b wrote:

Dear forum, whoever knows this please tell me!!!!!

Given two fpkm . e.g. fpkm 1=2922828 and fpkm 2=0, why cuffdiff does not calculate differential expression. those genes are listed in cuffdiff as not significant and the log2 fold change is infinite , either negative or positve...how do i consider them when i want to pull out the genes that are differentially expressed between treated and untreated samples?

how do i interpret these data?

thanks, ib ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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