Hi all, I have a dataset consisting of sequence data from specific viral genes that I'm trying to correlate to data from indicators of disease outcome (CD4+ count, viral load etc). Are there any packages currently available through bioconductor that would be suitable for exploring associations within the data? Many Thanks Ian Cheeseman Research Degree Student Room 360 London School of Hygiene & Tropical Medicine Department of Infectious and Tropical Diseases Pathogen Molecular Biology Unit Keppel Street London WC1E 7HT Office Tel: +44 (0) 207 6127829 Mobile Tel. +44 (0) 7855 424670

Dear Ian, I guess pretty much all of the regression and classification methods provided in R packages on CRAN and Bioconductor could be of potential use. Depending on your data, it would seem appropriate not to treat each sequence position and variant as independent, but to consider their phylogenetic tree. This paper and others by these authors might be relevant: http://nar.oxfordjournals.org/cgi/content/full/31/13/3850 Geno2pheno: estimating phenotypic drug resistance from HIV-1 genotypes N. Beerenwinkel et al. Best wishes Wolfgang > Hi all, > > I have a dataset consisting of sequence data from specific viral genes > that I'm trying to correlate to data from indicators of disease outcome > (CD4+ count, viral load etc). Are there any packages currently available > through bioconductor that would be suitable for exploring associations > within the data? > > Many Thanks > > Ian Cheeseman > > Research Degree Student > Room 360 > London School of Hygiene & Tropical Medicine > Department of Infectious and Tropical Diseases > Pathogen Molecular Biology Unit > Keppel Street > London WC1E 7HT > Office Tel: +44 (0) 207 6127829 > Mobile Tel. +44 (0) 7855 424670 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Best wishes Wolfgang ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber