Thank you Sean,
but i guess that the hypothesys is a little bit different.

i would obtain 1000 genes from the first comparisono and then i would like
to know which is the FC of the previous 1000 genes in the second comparison
and then a value in order to compare the two different FC (the second FC
respect the first FC).

This is what i would like to obtain.

Best regards.

2011/7/26 Sean Davis <sdavis2@mail.nih.gov>

> On Tue, Jul 26, 2011 at 5:50 AM, Alberto Goldoni
> <alberto.goldoni1975@gmail.com> wrote:
> > Dear Samuel,
> > i have affymetrix rattus norvegius chip.
> >
> > i have found 1000 interesting genes in the comparison 1 between
> > "hypertensive rats (A)" vs "standard rats (B)" and i would like to
> > understand the behaviour of these 1000 genes in the comparison 2
> > "hypertensive rats+omega3 (C)" vs "standard rats (B)"
> >
> > After that i would like to obtain a sort of "value" in order to estimate
> the
> > "% change" of each gene from the comparison 2 (C vs B) respect the
> > comparison 1 (A vs B).
>
> Hi, Alberto.
>
> It sounds like the biologic hypothesis that you want to test is that
> omega3 has an effect on some genes in hypertensive rats?  If that is
> correct, I would suggest doing the comparison of C vs A using limma or
> some other package for differential expression (perhaps the same way
> you compared A with B and C with B).
>
> Sean
>
> > best regards
> >
> > 2011/7/26 Samuel Wuest <wuests@tcd.ie>
> >
> >> Dear Alberto,
> >>
> >> I am not quite sure how your experimental design looks like in detail,
> >> but it seems to me that you have dual-label microarray data and an
> >> unconnected design with two factors (hence the two separate
> >> comparison?). If this is the case, then there is a very nice
> >> functionality in the limma package that is designed to make
> >> separate-channel analyses from unconnected designs, including
> >> appropriate between-array normalizations etc; thus, you can test any
> >> contrast you like and also interactions....
> >>
> >> Everything is nicely described in the limma users guide; simply type:
> >>
> >> library(limma)
> >> limmaUsersGuide()
> >>
> >> and check Chapter 9 " Separate Channel Analysis of Two-Color Data".
> >>
> >> Would this answer the question? Hope it helps anyway,
> >>
> >> Best, Sam
> >>
> >> On 26 July 2011 10:12, Alberto Goldoni <alberto.goldoni1975@gmail.com>
> >> wrote:
> >> > Dear all,
> >> > i have a doubt on the way to proceed in analyzing my data.
> >> >
> >> > Let me explain what i would like to obtain: i have 1000 genes obtained
> >> from
> >> > the comparison 1 (A vs B) and i would like to obtain the Fold Change
> and
> >> > pvalue of this 1000 genes in the comparison 2 (C vs B).
> >> >
> >> > After that what i'm gonna to do is to obtain a sort of "value" in
> order
> >> to
> >> > estimate the "% change" of each gene from the comparison 2 respect the
> >> > comparison 1 and i don't think that comparing the FC (experiment A)
> with
> >> the
> >> > FC (experiment B) is enought!
> >> >
> >> > Has anyone any comments or suggestions about how to extract a value
> >> > that allows me to evaluate the change of each gene obtained in the
> >> > comparison 2 respect the comparison 1?
> >> >
> >> > Thanks to anyone who will help me.
> >> >
> >> > Best regards.
> >> >
> >> > --
> >> > -----------------------------------------------------
> >> > Dr. Alberto Goldoni
> >> > Parma, Italy
> >> > -----------------------------------------------------
> >> >
> >> >        [[alternative HTML version deleted]]
> >> >
> >> > _______________________________________________
> >> > Bioconductor mailing list
> >> > Bioconductor@r-project.org
> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> > Search the archives:
> >> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >> >
> >>
> >>
> >>
> >> --
> >> -----------------------------------------------------
> >> Samuel Wuest
> >> Smurfit Institute of Genetics
> >> Trinity College Dublin
> >> Dublin 2, Ireland
> >> Phone: +353-1-896 2444
> >> Web: http://www.tcd.ie/Genetics/wellmer-2/index.html
> >> Email: wuests@tcd.ie
> >> ------------------------------------------------------
> >>
> >
> >
> >
> > --
> > -----------------------------------------------------
> > Dr. Alberto Goldoni
> > Parma, Italy
> > -----------------------------------------------------
> >
> >        [[alternative HTML version deleted]]
> >
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor@r-project.org
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor
> >
>



-- 
-----------------------------------------------------
Dr. Alberto Goldoni
Parma, Italy
-----------------------------------------------------

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