Being a big believer in single-channel analysis of loop designs, I used lmscFit to analyze my loop design data. All went well until the investigator requested the normalized single channel data. Since lmscFit actually operates on M and A, we took the same MAlist, and created R and G using RG.MA. To check the computation, we then computed the treatment means by hand for a few genes. These did not work out to the same treatment means obtained from lmscFit (using model ~-1+Trt). I hope that someone can explain why these are not equal. (And I really hope that this is not another case where I did not read the documentation sufficiently carefully.) Naomi S. Altman 814-865-3791 (voice) Associate Professor Dept. of Statistics 814-863-7114 (fax) Penn State University 814-865-1348 (Statistics) University Park, PA 16802-2111

Hi, This refers to selection of cutoff for SELDI-TOF data as described in the chapter 6 of Gentleman et al (Bioinformatics and Comp Bio Solutions using R and Bioconductor). On page 101 (Fig 6.5: cutpoint vs. average sd), the first local minimum around 400 is chosen. However, in another dataset, page 106 (Fig 6.7) the first local minimum around 350 is _not_ selected. Instead the chosen cutoff 1000 is far too much to the right and not even on an local minimum. I am unable to reconcile the two instances of cutoff choice. Thanks for any explanation. Saroj