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