Dear Sir/Madam: Thank you very much in advance for your help ! Mr. Robert Gentleman instructed me to contact you (Bioconductor mailing list)to ask for help regarding Library of new chip types (Human/Mouse/Rat Gene 1.0 ST Array) in Bioconductor R. Our ArrayTrack, an FDA microarray software, relay on your Bio- conductor to convert affy cel file to probe sets file. However, we found that Human/Mouse/Rat Gene 1.0 ST Array types are not in your R library. http://www.fda.gov/nctr/science/centers/toxicoinformatics/ArrayTrack/i nd ex.htm The design of Affymetrix array types Human/Mouse/Rat Gene 1.0 ST Array is very different from the older ones. One of the key changes is that no matching MM probes are used for every PM probe. So, the absence of MM probes has implication for some summarization algorithms and also affect background subtraction procedures. For example, MAS5 implemented in Bioconductor are affected by the change. Therefore, MAS 5 algorithms can not be run on the Exon and Gene arrays. However, RMA, d-chip and plier should still be OK . We could manually download the corresponding CDF file from affy's web site and then read the CDF into R, and then run rma() etc. However, it will not meet customers request to download cdf file from your library automatically. http://rss.acs.unt.edu/Rdoc/library/ We believe you have been working on it! Nerveless, We would like to know when Human/Mouse/Rat Gene 1.0 ST Array cdfs files would be available to the public? Therefore we will anticipate it. Thank you so much for your rich resources! we all benefit from Bioconductor R programs! We are looking forward to your help!!! Best Regards, Hong -------------------------------------------------------- Dr. Hong Fang Senior Technical Specialist Manger, Bioinformatics ICF International at NCTR National Center for Toxicological Research (NCTR) Food and Drug Administration (FDA) 3900 NCTR Road Jefferson, AR 72079 Tel: 870-543-7538 Fax: 870-543-7382 Fax: hong.fang at fda.hhs.gov