[BioC] lmFit: how method I use in non-Affy single channel

[Marcelo Luiz de Laia]

Dear limma users,

The function lmFit have 3 methods. One, default, use gls.series and 
another, robust, use rlm.series from MASS package. In help, gls.series 
is mentioned to be used in hight correlation between spots replication. 
In my case I dont have this.

I visited the help files but I dont get knowledge for decide how I use 
in my data set. The method robust show more differentially genes and a 
"B" value around 50. The P.value was around 1E-016. This is  OK?

Please, if you have a time, tell me how this method I use. Or I try they 
and use how I like?

I have a single channel data set from filters (nylon membrane). Each 
experiment have 6 biological repetition and each gene is printed 2 times 
in each filter. I have one reference and 3 times points. I construct a 
contrast matrix and do all constrast. I use topTable and heatDiagram to 
get genes.

Thanks

Marcelo