Hi, Has anyone given thought to adapting bioconductor to assist in the interpretation of protein and peptide mass spectrometry data? Thanks, Chris Paulse _________________________________________________________________ Help STOP SPAM: Try the new MSN 8 and get 2 months FREE*

i have used the Biobase package to keep spectra as exprSet objects. not much adaptation was required. in the exprs slot I use the gene dimension (rows) for the different spectral mass and the array dimension (columns) for the different spectra. the subject information goes into the phenoData slot. you can then, for example, 1) use genefilter to do feature selection, 2) choose from the many classification functions in R to classify samples, 3) take advantage of R graphics. 4) etc.. let me know if you want to discuss this further... rafael On Thu, 16 Jan 2003, Chris Paulse wrote: > Hi, > Has anyone given thought to adapting bioconductor to assist in the > interpretation of protein and peptide mass spectrometry data? > > Thanks, > Chris Paulse > > _________________________________________________________________ > Help STOP SPAM: Try the new MSN 8 and get 2 months FREE* > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >

What sort of stuff were you thinking of? 2D gels, Maldi/Seldi-tof? I have some experience with seldi-tof, but basically relying on commercial software for biomarker identification and from there it is pretty much standard classification. There would certainly be some interest in issues like, - baseline subtraction - peak detection etc, but there are far too many other things on my plate right now to do much more than pass along advice Robert On Thu, Jan 16, 2003 at 08:45:48AM -0800, Chris Paulse wrote: > Hi, > Has anyone given thought to adapting bioconductor to assist in the > interpretation of protein and peptide mass spectrometry data? > > Thanks, > Chris Paulse > > _________________________________________________________________ > Help STOP SPAM: Try the new MSN 8 and get 2 months FREE* > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor -- +--------------------------------------------------------------------- ------+ | Robert Gentleman phone : (617) 632-5250 | | Associate Professor fax: (617) 632-2444 | | Department of Biostatistics office: M1B20 | Harvard School of Public Health email: rgentlem@jimmy.dfci.harvard.edu | +--------------------------------------------------------------------- ------+