Dear Gordon: I tried to use ebayes() method to pick differential expressed genes for our two color cDNA microarray data analysis. Our expreiment is designed to anaylysis the influense of one chemical on cotton genes. It is a Single-Sample Expreiment and two RNA sources are comapred deirectly on 3 biological replicates through time course. But we don't have complete cotton gene library. So we hand pick around 200 genes that we expect to be differentiall expressed and print them 12 times (technical replicates) on the same slide. I have following questions: (1) Based our expreiment design, is it still suitable to use ebayes() method to pick differentially expressed genes for our data? (2)I took a look at help file for ebayes() and found out the default vale for proportion is 0.01. What value should I set for proportion for our case? Do I need to change default value for stdev.coef.lim? I highly appreciate your help. Hua Microarray Core Facility Department of Biochemistry and Molecular Biology Oklahoma State University 348E Noble Research Center Stillwater, OK 74078 Phone: 405-744-6209 Fax: 405-744-7799

At 01:42 AM 20/07/2004, Hua Weng wrote: >Dear Gordon: > >I tried to use ebayes() method to pick differential expressed genes for our >two color cDNA microarray data analysis. Our expreiment is designed to >anaylysis the influense of one chemical on cotton genes. It is a >Single-Sample Expreiment and two RNA sources are comapred deirectly on 3 >biological replicates through time course. But we don't have complete cotton >gene library. So we hand pick around 200 genes that we expect to be >differentiall expressed and print them 12 times (technical replicates) on >the same slide. I have following questions: > >(1) Based our expreiment design, is it still suitable to use ebayes() method >to pick differentially expressed genes for our data? > >(2)I took a look at help file for ebayes() and found out the default vale >for proportion is 0.01. What value should I set for proportion for our case? >Do I need to change default value for stdev.coef.lim? You can still use ebayes(), but use the moderated t-statistic rather than the log-odds (B-statistic) because the former doesn't require an estimate of the proportion of differentially expressed genes. A more subtle question is to normalize data where most or all of the genes are differentially expressed. Gordon >I highly appreciate your help. > >Hua > >Microarray Core Facility >Department of Biochemistry and Molecular Biology > >Oklahoma State University > >348E Noble Research Center > >Stillwater, OK 74078 > > Phone: 405-744-6209 > >Fax: 405-744-7799