Hi Joyce, > 1, I use read.marrayRaw() to read into my data into R, and found I have a lot > of NA value, I would like to know what is the algorithm to calcualte this > value. It is log ratio, do you also have certain kind of thresh value to cut > off? read.marrayRaw doesn't do any thresholding or cutoff. The M values are calculated by M = log(Rf - Rb / Gf- Gb) Now if your Rb > Rf than is will generate NA values. > 2, I use loess algorithm to normalize my data, and did correlation between > replicates, they all have pretty good correlation, but I found that among > different samples(not replicates), their correlation are still good, which > does not make sense. Are you using a common reference design? Are you calculating correlation between log-ratios or log-intensities? You will see high correlation with log-intensities. But for log-ratios, it will depends on the number of your DE genes. > 3, I use maPlot() to plot pre-normalization and post- normalization(which are > implemented in PrintTip algorithm). I did see some changes between, but I saw > the line yield down, but dot just yield a little bit more. I don't quite follow your question. The loess line should look horizontal post-normalization. Will take a look at your data files. Cheers Jean