I am trying to recreate some results from an external microarray dataset and they use Storey and Tibshirani's False Discovery Rate for multiple testing correction. Is this implemented in Bioconductor at all? Having a quick glance at the paper it looks like it is related to Benjamin Hochberg but not quite the same. Thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}

Hi Daniel, Storey's group released a package in CRAN called qvalue. Cheers, Alex -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Daniel Brewer Sent: 30 January 2008 10:16 To: bioconductor at stat.math.ethz.ch Subject: [BioC] Storey and Tibshirani FDR I am trying to recreate some results from an external microarray dataset and they use Storey and Tibshirani's False Discovery Rate for multiple testing correction. Is this implemented in Bioconductor at all? Having a quick glance at the paper it looks like it is related to Benjamin Hochberg but not quite the same. Thanks -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:9}}

Hi Daniel, You could use the Qvalue package in R to implement the Storey and Tibshirani's approach. Benjamini and Hochberg's method is a special case of the Storey and Tibsirani's that you can apply with the qvalue function by fixing lambda to 0. Example of use: ## p is the vector containing the pvalues to correct for multiple testing >library(qvalue) >qobj = qvalue(p) ## will return an object containing the corrected pvalues with the default Storey and Tibsirani's approach. >qobj$qvalue ## is the vector containing the corrected pvalues = qvalue >qobj = qvalue(p,lambda=0) ## will return an object containing the corrected pvalues according to Benjamini and Hochberg Hope this helps, Naira Daniel Brewer wrote: > I am trying to recreate some results from an external microarray dataset > and they use Storey and Tibshirani's False Discovery Rate for multiple > testing correction. Is this implemented in Bioconductor at all? Having > a quick glance at the paper it looks like it is related to Benjamin > Hochberg but not quite the same. > > Thanks > > -- ================================================================== Naira Naouar Tel:+32 (0)9 331 38 63 VIB Department of Plant Systems Biology, Ghent University Technologiepark 927, 9052 Gent, BELGIUM nanao at psb.ugent.be http://www.psb.ugent.be