[BioC] FW: how to 'bootstrap' expression data?

Johnstone, Alice Alice.Johnstone at esr.cri.nz
Wed Sep 26 06:50:05 CEST 2007

> -----Original Message-----
> From: Kasper Daniel Hansen [mailto:khansen at stat.Berkeley.EDU]
> Sent: Wednesday, 26 September 2007 4:25 p.m.
> To: Johnstone, Alice
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] how to 'bootstrap' expression data?
> On Sep 25, 2007, at 3:48 PM, Johnstone, Alice wrote:
> > Hi,
> > I have a set of Affymetrix array data 3 groups  (two treatment one
> > control) of 5 individuals in each.  I have analysed by fitting my 
> > model with a contrast of treatment-control, and
> treatment2-control to
> > the linear model, using an eBayes correction, then listed the top 
> > genes using topTable.  I have been asked to 'bootstrap' my
> results to
> > 'weed-out' false positives before QPCR validation.
> > Is this a necessary step?  And if so at what stage do I use
> it and how
> > do I go about applying it to my expression data to find the 
> > differentially expressed genes?
> > My background is definitely not in statistics so any discussion or 
> > pointers would be gratefully received!
> Why don't you ask the people who told you to do this: they should be 
> in a prime position to know what they mean.

The purpose is to multi-sample the same data at n-1 repeatedly which
would give you a robust list of genes that then would stay within the
top 100, say.  Hence giving more 'real' genes and less false positives
due to the odd aberrant probe signal. My question was about the
application of the idea. Ie whether the method I've used covered this
sufficiently, or is it a good idea to bootstrap? and if so a point
towards the correct packages/guide because Im unsure how to apply it to
expression data.

> > Thank you
> >
> > Alice
> >
> > P Think before you print
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> So do you think this applies to an email list?
> Kasper

I apologise for the addition message at the end of my post, so Kasper if
you can suggest a way to turn off the comments automatically placed by
our IT department to every external email, then go ahead.  Otherwise
please just comments on my questions/problem would be appreciated.
Thank you.

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