Dear Peter, > > i got 70458 transcripts of one worm by de novo assembly, > but i found 11825 of them are Escherichia contamination. > i think if i donot remove them,it will bother the later analysis, > e.g. > normalization ?? As normalization relays mainly on intensities (except methods when you select control probes) you should leave E. coli data for normalization and remove it afterwards. These 1/7 non interesting for you probes would compromise further differential expression analysis (inflated fdr cutoff value). Best Wishes, -- Dr Maciej Jonczyk, Department of Plant Molecular Ecophysiology Faculty of Biology, University of Warsaw 02-096 Warsaw, Miecznikowa 1 Poland -- This email was Anti Virus checked by Astaro Security Gateway. http://www.astaro.com