(no subject)
0
0
Entering edit mode
Paul Boutros ▴ 340
@paul-boutros-371
Last seen 9.6 years ago
>Date: Thu, 9 Sep 2004 22:01:22 +1000 (EST) >From: "Gordon K Smyth" <smyth@wehi.edu.au> >Subject: Re: [BioC] Finding and controlling for dye bias in Limma >To: "Sean Davis" <sdavis2@mail.nih.gov> >Cc: Bioconductor <bioconductor@stat.math.ethz.ch> > >> We have several samples hybed on two-color arrays (treated versus >> untreated). Half are in dye-swap. Can we use Limma to estimate the >> effect of dye-bias? > >Yes > >> A design matrix might look something like: >> >> Array Treatment Dye-bias >> 1 1 0 >> 2 1 0 >> 3 1 0 >> 4 1 0 >> 5 -1 1 >> 6 -1 1 >> 7 -1 1 >> 8 -1 1 >> >> The second coefficient would be significant for "dye-biased genes" >> while the first would be treatment effect while controlling for dye >> bias? Do I understand correctly? > >No, the Dye-bias column should be all 1's. If he has half the samples in each dye-swap status, would it be alternating 1's and -1's? Array Treatment Dye-bias 1 1 1 2 1 -1 3 1 1 4 1 -1 5 -1 1 6 -1 -1 7 -1 1 8 -1 -1 >Gordon > >> Thanks, >> Sean
limma limma • 602 views
ADD COMMENT

Login before adding your answer.

Traffic: 725 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6