Hi All, We will be updating the Bioconductor website to allow searching and downloading of packages and documents (e.g. package vignettes) based on keywords. Keywords might reflect the type of biological data (e.g. cDNA array data, Affy data, sequence data), the type of analysis (e.g. normalization), etc. Here is an initial and unstructured list of keywords to start/continue discussion. Please e-mail your suggestions regarding keywords and how to structure the list. Best, Sandrine cDNA arrays oligonucleotide arrays/Affymetrix datasets novice/basics infrastructure/base data management input & output preprocessing/normalization graphics/plotting annotation differential gene expression/gene screening/gene filtering clustering classification resampling ---------------------------------------------------------------------- --------- Sandrine Dudoit, Ph.D. E-mail: sandrine@stat.berkeley.edu Assistant Professor Tel: (510) 643-1108 Division of Biostatistics Fax: (510) 643-5163 School of Public Health http://www.stat.berkeley.edu/~sandrine University of California, Berkeley 140 Earl Warren Hall, #7360 Berkeley, CA 94720-7360 ---------------------------------------------------------------------- ---------

>>>>> "sandrine" == Sandrine Dudoit <sandrine@stat.berkeley.edu> writes: sandrine> Hi All, sandrine> We will be updating the Bioconductor website to allow searching and downloading sandrine> of packages and documents (e.g. package vignettes) based on keywords. sandrine> Keywords might reflect the type of biological data (e.g. cDNA array data, sandrine> Affy data, sequence data), the type of analysis (e.g. normalization), etc. sandrine> Here is an initial and unstructured list of keywords to start/continue sandrine> discussion. Please e-mail your suggestions regarding keywords and how to structure sandrine> the list. sandrine> Best, sandrine> Sandrine sandrine> cDNA arrays sandrine> oligonucleotide arrays/Affymetrix for completeness: radioactive filters (i.e. research genetics membrane arrays). Has anyone worked with output from an Agilent system? sandrine> datasets sandrine> novice/basics sandrine> infrastructure/base sandrine> data management sandrine> input & output sandrine> preprocessing/normalization sandrine> graphics/plotting replace with visualization? sandrine> annotation sandrine> differential gene expression/gene screening/gene filtering sandrine> clustering sandrine> classification sandrine> resampling "inference", i.e. Mark vdL's work, if it ever gets integrated (not simple to fix up a good elicitation UI, but...). "bayesian" (and empirical bayes, which isn't, for some of the normalization methods?) best, -tony -- A.J. Rossini Rsrch. Asst. Prof. of Biostatistics U. of Washington Biostatistics rossini@u.washington.edu FHCRC/SCHARP/HIV Vaccine Trials Net rossini@scharp.org -------------- http://software.biostat.washington.edu/ ---------------- FHCRC: M-W: 206-667-7025 (fax=4812)|Voicemail is pretty sketchy/use Email UW: Th: 206-543-1044 (fax=3286)|Change last 4 digits of phone to FAX (my friday location is usually completely unpredictable.)