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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