[BioC] Question on LIMMA
James W. MacDonald
jmacdon at med.umich.edu
Tue Jul 7 14:32:05 CEST 2009
Francisco Javier Burguillo wrote:
> Dear colleages,
> I can not uderstand a result I have. I made t-permutations and LIMMA to
> find differentially expressed genes on the same dataset. Is it posible I
> can have
> a gene which is overexpressed using t-permutations (t value = + something)
> and underespressed using LIMMA (Statistic= - something) ?
That's highly unlikely - the numerator (which is responsible for the
sign of the statistic) is identical in both cases. The only differences
are slight changes in how the denominator is computed, and what
distribution the t-statistics are compared against.
It's more likely that you have e.g. experimental - control in one case
and control - experimental in the other. However, without seeing your
code that's just a guess.
> Sorry but I can not fully understand the LIMMA algorithm yet.
> Many thanks,
> Fco. Javier Burguillo
> Departamento de Química Física
> Facultad de Farmacia
> Universidad de Salamanca
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> Search the archives:
James W. MacDonald, M.S.
University of Michigan
Department of Human Genetics
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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