[BioC] is-normalisation-really-required

Gorjanc Gregor Gregor.Gorjanc at bfro.uni-lj.si
Wed Apr 13 14:03:19 CEST 2005


You might try analysis with and without normalization and take
a look at the results. If they say the same thing than I would 
say, no it is not necessary to do normalization.

> dear friends
> i have situation, where i thought its ok for me not to
> do normalisation, i am afraid i may be wrong. i want
> your advice in this regard.
> we performed a wild type - mutant, dye-swap
> experiment.
> when we analysed the intensity values, they were
> consistant among the two experiment (dye-swap). ie.,
> almost same values for mutants in both the experiments
> of the dye-swap.
> since the values are almost same, i thought there
> might not be any dye-bias, so i just went ahead,
> averaged the two values, found out their ratio and
> filtered genes with 2 fold change.
> so i have done this without normalisation.
> i am afraid, i might be wrong, my 2 fold chaging genes
> might be wrong...
> kindly give me your advice in this regard.
> i did analyse the data with limma, but the topTable
> genes there never correlates with my 2 fold genes.
> kindly correct me.
> thanks
> vijay
> graduate student
> department of biological sciences
> the university of southern mississippi

Lep pozdrav / With regards,
    Gregor Gorjanc

University of Ljubljana
Biotechnical Faculty       URI: http://www.bfro.uni-lj.si/MR/ggorjan
Zootechnical Department    email: gregor.gorjanc <at> bfro.uni-lj.si
Groblje 3                  tel: +386 (0)1 72 17 861
SI-1230 Domzale            fax: +386 (0)1 72 17 888

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