Thanks, it was really helpful.
Priscila

On Thu, Jan 8, 2009 at 3:58 PM, Jenny Drnevich <drnevich@illinois.edu>wrote:

> Hi Priscila,
>
> The robustspline method for normalization has nothing to do with the
> lmFit(method="robust"). lmFit can either fit the model using a least squares
> regression or a robust regression, which down-weights replicates that are
> different from the other replicates. Whether or not to use
> lmFit(method="robust") doesn't depend on which normalization method you use,
> but rather (IMO) how many replicates you have. If you have a relatively
> large number of replicates, say 6 or more, then the robust fitting of the
> model may help to remove true outliers from affecting the data. However, if
> you only have 3 replicates, as is usual for microarray experiments, using
> the robust estimation may remove real variation in your samples and lead to
> more false-positives.
>
> That's my take on the situation...
> Jenny
>
> At 10:49 AM 1/8/2009, Priscila Grynberg wrote:
>
>> Content-Type: text/plain
>> Content-Disposition: inline
>> Content-length: 1308
>>
>>
>> Hi BioCs,
>> I have a doubt about this function.
>>
>> I'm working with a two-channel dye-swap microarray experiments. After
>> testing all normalization methods, I conclude that the robustspline method
>> was the best for my data. After normalizing, I did the statistical
>> analysis
>> using the lmFit and eBayes functions.
>>
>> My commands were:
>>
>> fit <- lmFit(MA, design, ndups=2, spacing=12, cor=corfit$consensus)
>>
>> fit2 <- eBayes(fit)
>>
>> Everything worked just fine. However, I read the lmFit help and a doubt
>> came
>> up:
>>
>>
>> lmFit(object,design=NULL,ndups=1,spacing=1,block=NULL,correlation,weights=NULL,
>> method="ls",...)
>>
>> method: character string, "ls" for least squares or "robust" for robust
>> regression
>>
>> Then, I repeat the same commands, but changing the parameter "method",
>> since
>> I used the robustspline method for normalization. I got different top 100
>> genes most differentially expressed. And now I really confused. I don't
>> know
>> what to do with this "method" parameter.
>>
>> I hope someone can explain to me!
>>
>> Thanks,
>>
>> Priscila
>>
>>
>>
>>
>> --
>> Priscila Grynberg, B.Sc., M.Sc.
>> Doutoranda em Bioinformática (Bioinformatics D.Sc student)
>> Laboratório de Genética Bioquímica
>> Universidade Federal de Minas Gerais
>> Tel: +55 31 3409-2628
>> CV: http://lattes.cnpq.br/8808643075395963
>>
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>>
>>
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>>
>
> Jenny Drnevich, Ph.D.
>
> Functional Genomics Bioinformatics Specialist
> W.M. Keck Center for Comparative and Functional Genomics
> Roy J. Carver Biotechnology Center
> University of Illinois, Urbana-Champaign
>
> 330 ERML
> 1201 W. Gregory Dr.
> Urbana, IL 61801
> USA
>
> ph: 217-244-7355
> fax: 217-265-5066
> e-mail: drnevich@illinois.edu
>



-- 
Priscila Grynberg, B.Sc., M.Sc.
Doutoranda em Bioinformática (Bioinformatics D.Sc student)
Laboratório de Genética Bioquímica
Universidade Federal de Minas Gerais
Tel: +55 31 3409-2628
CV: http://lattes.cnpq.br/8808643075395963

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