Gregor.Gorjanc at bfro.uni-lj.si
Wed Apr 13 14:29:16 CEST 2005
> -----Original Message-----
> From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
> Sent: sre 2005-04-13 14:16
> To: Gorjanc Gregor
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] is-normalisation-really-required
> On Apr 13, 2005, at 8:03 AM, Gorjanc Gregor wrote:
> > Hi!
> > 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.
> So, if the two results agree, then the results with normalization are
> correct; if not then the results with normalization are still correct.
> Sounds like we are pretty much stuck with normalization....
Why should one do normalization if the results aren't different. But, in
that case it really does not matter and one can do it or not.
>> 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
>> 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.
>> graduate student
>> department of biological sciences
>> the university of southern mississippi
>> MS, USA
> 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
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
More information about the Bioconductor