[BioC] Analysis of Differentially Expressed Genes using Microarray Technology

[Eleonora Lusito]

Dear Dott. Friedman,
I TOTALLY AGREE with you!!
I stressed the people gave me the data to do at least 3 replicates per
condition but samples are not available anymore, unfortunately..

Best

E.

 Richard Friedman (friedman at cancercenter.columbia.edu) wrote:
 >
 > Dear Eleonora,
 >
 > The results will not be reliable because you will not
 > take the variability (both biological and technical) into account.
 > One replicate each will only give you log Foldchanges, but no
 > measure of the variability. Whether you go ahead or not
 > is up to you but I try to avoid doing this whenever possible
 > and I also tell the people that any such results come with
 > a big question mark.
 >
 > with hope that this helps,
 > Rich
 > Richard A. Friedman, PhD
 > Associate Research Scientist,
 > Biomedical Informatics Shared Resource
 > Herbert Irving Comprehensive Cancer Center (HICCC)
 > Lecturer,
 > Department of Biomedical Informatics (DBMI)
 > Educational Coordinator,
 > Center for Computational Biology and Bioinformatics (C2B2)/
 > National Center for Multiscale Analysis of Genomic Networks (MAGNet)
 > Room 824
 > Irving Cancer Research Center
 > Columbia University
 > 1130 St. Nicholas Ave
 > New York, NY 10032
 > (212)851-4765 (voice)
 > friedman at cancercenter.columbia.edu
 > http://cancercenter.columbia.edu/~friedman/
 >
 > In memoriam, Ray Bradbury
 >
 > On Sep 10, 2012, at 2:38 PM, Eleonora Lusito wrote:
 >
 > > Dear BioC users, I have a question regarding microarray data analysis
(Human
 > > Affymetrix one color). My point is that I have just 1 sample TREATMENT
and 1
 > > sample REFERENCE. Neither technical replicates nor biological replicates
are
 > > available. A statistical test to find differentially expressed genes
between
 > > the two conditions seems to me impossible (even the simple t-test) due to
the
 > > absence of replicates. People who asked me to do the analysis were
interested
 > > only in finding the genes changing between the two conditions. In this
 > > conditions, in my opinion only the fold change is possible just to give a
 > > general view of the behavior of the genes. Any other suggestion about
this
 > > issue?
 > >
 > > Thanks a lot
 > >
 > > E.
 > >
 > > --
 > > Eleonora Lusito
 > > Computational Biology PhD student
 > > Molecular Medicine Program
 > > via Ripamonti 435, 20141 Milano, Italy
 > >
 > > Phone number: +390294375160
 > > e-mail: eleonora.lusito at ieo.eu
 > >
 > > _______________________________________________
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 > > Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor
 >
 >

-- 
Eleonora Lusito
Computational Biology PhD student
Molecular Medicine Program
via Ripamonti 435, 20141 Milano, Italy

Phone number: +390294375160
e-mail: eleonora.lusito at ieo.eu