[BioC] help to proceed with the interpretation of an analysis

Samuel Wuest wuests at tcd.ie
Tue Jul 26 11:27:38 CEST 2011

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:


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 at 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]]
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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 at tcd.ie

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