> -----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 > > This e-mail transmission and any attachments that accompany it may > > contain information that is privileged, confidential or otherwise > > exempt from disclosure under applicable law and is intended > solely for > > the use of the individual(s) to whom it was intended to be > addressed. > > If you have received this e-mail by mistake, or you are not the > > intended recipient, any disclosure, dissemination, distribution, > > copying or other use or retention of this communication or its > > substance is prohibited. If you have received this communication in > > error, please immediately reply to the author via e-mail that you > > received this message by mistake and also permanently delete the > > original and all copies of this e-mail and any attachments > from your > > computer. Thank you. > > 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.